1. HiContacts
  2. NAMESPACE
Browse code

fix: add missing import

js2264 authored on 23/05/2023 16:12:52
Showing 1 changed files
NAMESPACE
History View file @ 689e754
... ... 
@@ -42,6 +42,7 @@ import(stringr)
42 42 
 import(tibble)
43 43 
 import(tidyr)
44 44 
 importFrom(BiocGenerics,normalize)
45 
+importFrom(BiocGenerics,path)
45 46 
 importFrom(BiocIO,import)
46 47 
 importFrom(BiocParallel,bplapply)
47 48 
 importFrom(BiocParallel,bpparam)
Browse code

fix: add S4Vectors::mcols to NAMESPACE

js2264 authored on 28/04/2023 17:39:03
Showing 1 changed files
NAMESPACE
History View file @ d2858a7
... ... 
@@ -58,6 +58,7 @@ importFrom(IRanges,coverage)
58 58 
 importFrom(Matrix,sparseMatrix)
59 59 
 importFrom(RSpectra,eigs_sym)
60 60 
 importFrom(S4Vectors,SimpleList)
61 
+importFrom(S4Vectors,mcols)
61 62 
 importFrom(S4Vectors,metadata)
62 63 
 importFrom(S4Vectors,queryHits)
63 64 
 importFrom(SummarizedExperiment,assay)
Browse code

fix: merge is now a method

js2264 authored on 24/04/2023 16:44:41
Showing 1 changed files
NAMESPACE
History View file @ 6f861ec
... ... 
@@ -20,7 +20,6 @@ export(getCompartments)
20 20 
 export(getDiamondInsulation)
21 21 
 export(getLoops)
22 22 
 export(localDistanceLaw)
23 
-export(merge)
24 23 
 export(plot4C)
25 24 
 export(plotPs)
26 25 
 export(plotPsSlope)
... ... 
@@ -33,6 +32,7 @@ export(virtual4C)
33 32 
 exportMethods(aggregate)
34 33 
 exportMethods(coverage)
35 34 
 exportMethods(distanceLaw)
35 
+exportMethods(merge)
36 36 
 exportMethods(montage)
37 37 
 exportMethods(normalize)
38 38 
 exportMethods(plotMatrix)
Browse code

bump to 1.1.4

js2264 authored on 12/04/2023 13:20:40
Showing 1 changed files
NAMESPACE
History View file @ 7018e3e
... ... 
@@ -31,6 +31,7 @@ export(scalogram)
31 31 
 export(subsample)
32 32 
 export(virtual4C)
33 33 
 exportMethods(aggregate)
34 
+exportMethods(coverage)
34 35 
 exportMethods(distanceLaw)
35 36 
 exportMethods(montage)
36 37 
 exportMethods(normalize)
Browse code

fix: getLoops now redirects to HiCool

js2264 authored on 12/04/2023 13:18:31
Showing 1 changed files
NAMESPACE
History View file @ caa2c7b
... ... 
@@ -9,6 +9,8 @@ export(boost)
9 9 
 export(bwrColors)
10 10 
 export(cisTransRatio)
11 11 
 export(coarsen)
12 
+export(contacts_yeast)
13 
+export(contacts_yeast_eco1)
12 14 
 export(coolerColors)
13 15 
 export(despeckle)
14 16 
 export(detrend)
... ... 
@@ -16,6 +18,7 @@ export(divide)
16 18 
 export(getBorders)
17 19 
 export(getCompartments)
18 20 
 export(getDiamondInsulation)
21 
+export(getLoops)
19 22 
 export(localDistanceLaw)
20 23 
 export(merge)
21 24 
 export(plot4C)
Browse code

fix: put GenomicFeatures in Suggests

js2264 authored on 29/03/2023 15:18:19
Showing 1 changed files
NAMESPACE
History View file @ ead8332
... ... 
@@ -41,7 +41,6 @@ importFrom(BiocGenerics,normalize)
41 41 
 importFrom(BiocIO,import)
42 42 
 importFrom(BiocParallel,bplapply)
43 43 
 importFrom(BiocParallel,bpparam)
44 
-importFrom(GenomicFeatures,genes)
45 44 
 importFrom(GenomicRanges,GRanges)
46 45 
 importFrom(GenomicRanges,countOverlaps)
47 46 
 importFrom(GenomicRanges,end)
Browse code

feat: switch distanceLaw methods for HiCExp/PairsFile

js2264 authored on 15/03/2023 09:50:52
Showing 1 changed files
NAMESPACE
History View file @ d1d61cc
... ... 
@@ -12,7 +12,6 @@ export(coarsen)
12 12 
 export(coolerColors)
13 13 
 export(despeckle)
14 14 
 export(detrend)
15 
-export(distanceLaw)
16 15 
 export(divide)
17 16 
 export(getBorders)
18 17 
 export(getCompartments)
... ... 
@@ -29,6 +28,7 @@ export(scalogram)
29 28 
 export(subsample)
30 29 
 export(virtual4C)
31 30 
 exportMethods(aggregate)
31 
+exportMethods(distanceLaw)
32 32 
 exportMethods(montage)
33 33 
 exportMethods(normalize)
34 34 
 exportMethods(plotMatrix)
... ... 
@@ -41,6 +41,7 @@ importFrom(BiocGenerics,normalize)
41 41 
 importFrom(BiocIO,import)
42 42 
 importFrom(BiocParallel,bplapply)
43 43 
 importFrom(BiocParallel,bpparam)
44 
+importFrom(GenomicFeatures,genes)
44 45 
 importFrom(GenomicRanges,GRanges)
45 46 
 importFrom(GenomicRanges,countOverlaps)
46 47 
 importFrom(GenomicRanges,end)
... ... 
@@ -79,6 +80,8 @@ importFrom(dplyr,slice_max)
79 80 
 importFrom(dplyr,summarize)
80 81 
 importFrom(dplyr,tally)
81 82 
 importFrom(ggrastr,geom_tile_rast)
83 
+importFrom(readr,DataFrameCallback)
84 
+importFrom(readr,read_tsv_chunked)
82 85 
 importFrom(scales,oob_censor)
83 86 
 importFrom(scales,oob_squish)
84 87 
 importFrom(scales,rescale)
Browse code

bump to 1.1.2

js2264 authored on 12/03/2023 16:27:11
Showing 1 changed files
NAMESPACE
History View file @ 0ad5782
... ... 
@@ -45,6 +45,7 @@ importFrom(GenomicRanges,GRanges)
45 45 
 importFrom(GenomicRanges,countOverlaps)
46 46 
 importFrom(GenomicRanges,end)
47 47 
 importFrom(GenomicRanges,findOverlaps)
48 
+importFrom(GenomicRanges,resize)
48 49 
 importFrom(GenomicRanges,seqnames)
49 50 
 importFrom(GenomicRanges,start)
50 51 
 importFrom(GenomicRanges,tileGenome)
Browse code

fix: rename `despeckled` scores to `<use.scores>.despeckled`

js2264 authored on 12/03/2023 16:23:53
Showing 1 changed files
NAMESPACE
History View file @ 8641ecc
... ... 
@@ -42,11 +42,14 @@ importFrom(BiocIO,import)
42 42 
 importFrom(BiocParallel,bplapply)
43 43 
 importFrom(BiocParallel,bpparam)
44 44 
 importFrom(GenomicRanges,GRanges)
45 
+importFrom(GenomicRanges,countOverlaps)
45 46 
 importFrom(GenomicRanges,end)
46 47 
 importFrom(GenomicRanges,findOverlaps)
47 48 
 importFrom(GenomicRanges,seqnames)
48 49 
 importFrom(GenomicRanges,start)
50 
+importFrom(GenomicRanges,tileGenome)
49 51 
 importFrom(IRanges,IRanges)
52 
+importFrom(IRanges,coverage)
50 53 
 importFrom(Matrix,sparseMatrix)
51 54 
 importFrom(RSpectra,eigs_sym)
52 55 
 importFrom(S4Vectors,SimpleList)
Browse code

doc: internal function overhaul

js2264 authored on 20/02/2023 14:33:00
Showing 1 changed files
NAMESPACE
History View file @ ccee17c
... ... 
@@ -9,14 +9,11 @@ export(boost)
9 9 
 export(bwrColors)
10 10 
 export(cisTransRatio)
11 11 
 export(coarsen)
12 
-export(contacts_yeast)
13 
-export(contacts_yeast_eco1)
14 12 
 export(coolerColors)
15 13 
 export(despeckle)
16 14 
 export(detrend)
17 15 
 export(distanceLaw)
18 16 
 export(divide)
19 
-export(full_contacts_yeast)
20 17 
 export(getBorders)
21 18 
 export(getCompartments)
22 19 
 export(getDiamondInsulation)
... ... 
@@ -40,7 +37,6 @@ import(InteractionSet)
40 37 
 import(stringr)
41 38 
 import(tibble)
42 39 
 import(tidyr)
43 
-importClassesFrom(GenomicRanges,GRanges)
44 40 
 importFrom(BiocGenerics,normalize)
45 41 
 importFrom(BiocIO,import)
46 42 
 importFrom(BiocParallel,bplapply)
Browse code

feat: 2-sides plotMatrix

js2264 authored on 13/02/2023 13:06:07
Showing 1 changed files
NAMESPACE
History View file @ 417a53c
... ... 
@@ -1,7 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(Contacts)
4 
-export(ShREC)
5 4 
 export(afmhotrColors)
6 5 
 export(autocorrelate)
7 6 
 export(bbrColors)
Browse code

fix: now detrend on [5-95%] values per diag

js2264 authored on 11/02/2023 16:49:35
Showing 1 changed files
NAMESPACE
History View file @ 7654ead
... ... 
@@ -80,6 +80,7 @@ importFrom(dplyr,slice_max)
80 80 
 importFrom(dplyr,summarize)
81 81 
 importFrom(dplyr,tally)
82 82 
 importFrom(ggrastr,geom_tile_rast)
83 
+importFrom(scales,oob_censor)
83 84 
 importFrom(scales,oob_squish)
84 85 
 importFrom(scales,rescale)
85 86 
 importFrom(scales,trans_breaks)
... ... 
@@ -87,6 +88,7 @@ importFrom(scales,trans_format)
87 88 
 importFrom(scales,unit_format)
88 89 
 importFrom(stats,cor)
89 90 
 importFrom(stats,median)
91 
+importFrom(stats,quantile)
90 92 
 importFrom(stats,rbinom)
91 93 
 importFrom(tibble,as_tibble)
92 94 
 importFrom(tibble,tibble)
Browse code

feat: coarsen function

js2264 authored on 06/02/2023 19:33:20
Showing 1 changed files
NAMESPACE
History View file @ 7c91724
... ... 
@@ -9,6 +9,7 @@ export(bgrColors)
9 9 
 export(boost)
10 10 
 export(bwrColors)
11 11 
 export(cisTransRatio)
12 
+export(coarsen)
12 13 
 export(contacts_yeast)
13 14 
 export(contacts_yeast_eco1)
14 15 
 export(coolerColors)
... ... 
@@ -62,6 +63,7 @@ importFrom(dplyr,bind_rows)
62 63 
 importFrom(dplyr,cur_data)
63 64 
 importFrom(dplyr,distinct)
64 65 
 importFrom(dplyr,filter)
66 
+importFrom(dplyr,full_join)
65 67 
 importFrom(dplyr,group_by)
66 68 
 importFrom(dplyr,group_modify)
67 69 
 importFrom(dplyr,group_split)
Browse code

minor fixes

js2264 authored on 26/01/2023 07:54:48
Showing 1 changed files
NAMESPACE
History View file @ fc4121d
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(Contacts)
4 
+export(ShREC)
4 5 
 export(afmhotrColors)
5 6 
 export(autocorrelate)
6 7 
 export(bbrColors)
... ... 
@@ -31,6 +32,7 @@ export(scalogram)
31 32 
 export(subsample)
32 33 
 export(virtual4C)
33 34 
 exportMethods(aggregate)
35 
+exportMethods(montage)
34 36 
 exportMethods(normalize)
35 37 
 exportMethods(plotMatrix)
36 38 
 import(HiCExperiment)
... ... 
@@ -39,6 +41,7 @@ import(stringr)
39 41 
 import(tibble)
40 42 
 import(tidyr)
41 43 
 importClassesFrom(GenomicRanges,GRanges)
44 
+importFrom(BiocGenerics,normalize)
42 45 
 importFrom(BiocIO,import)
43 46 
 importFrom(BiocParallel,bplapply)
44 47 
 importFrom(BiocParallel,bpparam)
... ... 
@@ -51,7 +54,6 @@ importFrom(IRanges,IRanges)
51 54 
 importFrom(Matrix,sparseMatrix)
52 55 
 importFrom(RSpectra,eigs_sym)
53 56 
 importFrom(S4Vectors,SimpleList)
54 
-importFrom(S4Vectors,aggregate)
55 57 
 importFrom(S4Vectors,metadata)
56 58 
 importFrom(S4Vectors,queryHits)
57 59 
 importFrom(SummarizedExperiment,assay)
... ... 
@@ -91,4 +93,3 @@ importFrom(tidyr,pivot_longer)
91 93 
 importFrom(tidyr,pivot_wider)
92 94 
 importFrom(utils,setTxtProgressBar)
93 95 
 importFrom(utils,txtProgressBar)
94 
-importMethodsFrom(BiocGenerics,normalize)
Browse code

fix divide function and other tiny bugs

js2264 authored on 18/01/2023 21:20:11
Showing 1 changed files
NAMESPACE
History View file @ 8a3cd74
... ... 
@@ -55,7 +55,6 @@ importFrom(S4Vectors,aggregate)
55 55 
 importFrom(S4Vectors,metadata)
56 56 
 importFrom(S4Vectors,queryHits)
57 57 
 importFrom(SummarizedExperiment,assay)
58 
-importFrom(WGCNA,cor)
59 58 
 importFrom(dplyr,arrange)
60 59 
 importFrom(dplyr,bind_rows)
61 60 
 importFrom(dplyr,cur_data)
... ... 
@@ -82,8 +81,14 @@ importFrom(scales,rescale)
82 81 
 importFrom(scales,trans_breaks)
83 82 
 importFrom(scales,trans_format)
84 83 
 importFrom(scales,unit_format)
84 
+importFrom(stats,cor)
85 
+importFrom(stats,median)
86 
+importFrom(stats,rbinom)
85 87 
 importFrom(tibble,as_tibble)
86 88 
 importFrom(tibble,tibble)
87 89 
 importFrom(tidyr,drop_na)
88 90 
 importFrom(tidyr,pivot_longer)
89 91 
 importFrom(tidyr,pivot_wider)
92 
+importFrom(utils,setTxtProgressBar)
93 
+importFrom(utils,txtProgressBar)
94 
+importMethodsFrom(BiocGenerics,normalize)
Browse code

add ICE normalization (normalize method)

js2264 authored on 18/01/2023 16:30:48
Showing 1 changed files
NAMESPACE
History View file @ c331e07
... ... 
@@ -31,6 +31,7 @@ export(scalogram)
31 31 
 export(subsample)
32 32 
 export(virtual4C)
33 33 
 exportMethods(aggregate)
34 
+exportMethods(normalize)
34 35 
 exportMethods(plotMatrix)
35 36 
 import(HiCExperiment)
36 37 
 import(InteractionSet)
Browse code

add boost and subsample

js2264 authored on 17/01/2023 20:16:01
Showing 1 changed files
NAMESPACE
History View file @ 38fa0a3
... ... 
@@ -5,6 +5,7 @@ export(afmhotrColors)
5 5 
 export(autocorrelate)
6 6 
 export(bbrColors)
7 7 
 export(bgrColors)
8 
+export(boost)
8 9 
 export(bwrColors)
9 10 
 export(cisTransRatio)
10 11 
 export(contacts_yeast)
... ... 
@@ -27,6 +28,7 @@ export(plotSaddle)
27 28 
 export(plotScalogram)
28 29 
 export(rainbowColors)
29 30 
 export(scalogram)
31 
+export(subsample)
30 32 
 export(virtual4C)
31 33 
 exportMethods(aggregate)
32 34 
 exportMethods(plotMatrix)
Browse code

doc: major rewriting

js2264 authored on 12/01/2023 21:45:38
Showing 1 changed files
NAMESPACE
History View file @ 1783a55
... ... 
@@ -23,8 +23,10 @@ export(merge)
23 23 
 export(plot4C)
24 24 
 export(plotPs)
25 25 
 export(plotPsSlope)
26 
+export(plotSaddle)
26 27 
 export(plotScalogram)
27 28 
 export(rainbowColors)
29 
+export(scalogram)
28 30 
 export(virtual4C)
29 31 
 exportMethods(aggregate)
30 32 
 exportMethods(plotMatrix)
... ... 
@@ -43,10 +45,6 @@ importFrom(GenomicRanges,findOverlaps)
43 45 
 importFrom(GenomicRanges,seqnames)
44 46 
 importFrom(GenomicRanges,start)
45 47 
 importFrom(IRanges,IRanges)
46 
-importFrom(InteractionSet,GInteractions)
47 
-importFrom(InteractionSet,anchors)
48 
-importFrom(InteractionSet,pairdist)
49 
-importFrom(InteractionSet,regions)
50 48 
 importFrom(Matrix,sparseMatrix)
51 49 
 importFrom(RSpectra,eigs_sym)
52 50 
 importFrom(S4Vectors,SimpleList)
Browse code

tidying up

js2264 authored on 12/01/2023 12:07:57
Showing 1 changed files
NAMESPACE
History View file @ a743be7
... ... 
@@ -24,6 +24,7 @@ export(plot4C)
24 24 
 export(plotPs)
25 25 
 export(plotPsSlope)
26 26 
 export(plotScalogram)
27 
+export(rainbowColors)
27 28 
 export(virtual4C)
28 29 
 exportMethods(aggregate)
29 30 
 exportMethods(plotMatrix)
... ... 
@@ -52,6 +53,7 @@ importFrom(S4Vectors,SimpleList)
52 53 
 importFrom(S4Vectors,aggregate)
53 54 
 importFrom(S4Vectors,metadata)
54 55 
 importFrom(S4Vectors,queryHits)
56 
+importFrom(SummarizedExperiment,assay)
55 57 
 importFrom(WGCNA,cor)
56 58 
 importFrom(dplyr,arrange)
57 59 
 importFrom(dplyr,bind_rows)
Browse code

feat: despeckle

js2264 authored on 10/01/2023 20:54:59
Showing 1 changed files
NAMESPACE
History View file @ d5cc841
... ... 
@@ -10,6 +10,7 @@ export(cisTransRatio)
10 10 
 export(contacts_yeast)
11 11 
 export(contacts_yeast_eco1)
12 12 
 export(coolerColors)
13 
+export(despeckle)
13 14 
 export(detrend)
14 15 
 export(distanceLaw)
15 16 
 export(divide)
Browse code

update doc

js2264 authored on 03/01/2023 21:33:00
Showing 1 changed files
NAMESPACE
History View file @ 86806ce
... ... 
@@ -22,6 +22,7 @@ export(merge)
22 22 
 export(plot4C)
23 23 
 export(plotPs)
24 24 
 export(plotPsSlope)
25 
+export(plotScalogram)
25 26 
 export(virtual4C)
26 27 
 exportMethods(aggregate)
27 28 
 exportMethods(plotMatrix)
... ... 
@@ -30,6 +31,7 @@ import(InteractionSet)
30 31 
 import(stringr)
31 32 
 import(tibble)
32 33 
 import(tidyr)
34 
+importClassesFrom(GenomicRanges,GRanges)
33 35 
 importFrom(BiocIO,import)
34 36 
 importFrom(BiocParallel,bplapply)
35 37 
 importFrom(BiocParallel,bpparam)
... ... 
@@ -56,6 +58,7 @@ importFrom(dplyr,cur_data)
56 58 
 importFrom(dplyr,distinct)
57 59 
 importFrom(dplyr,filter)
58 60 
 importFrom(dplyr,group_by)
61 
+importFrom(dplyr,group_modify)
59 62 
 importFrom(dplyr,group_split)
60 63 
 importFrom(dplyr,lead)
61 64 
 importFrom(dplyr,left_join)
... ... 
@@ -77,5 +80,6 @@ importFrom(scales,trans_format)
77 80 
 importFrom(scales,unit_format)
78 81 
 importFrom(tibble,as_tibble)
79 82 
 importFrom(tibble,tibble)
83 
+importFrom(tidyr,drop_na)
80 84 
 importFrom(tidyr,pivot_longer)
81 85 
 importFrom(tidyr,pivot_wider)
Browse code

doc update and centros_yeast data removed

js2264 authored on 02/01/2023 13:24:03
Showing 1 changed files
NAMESPACE
History View file @ baf8f9e
... ... 
@@ -14,6 +14,7 @@ export(detrend)
14 14 
 export(distanceLaw)
15 15 
 export(divide)
16 16 
 export(full_contacts_yeast)
17 
+export(getBorders)
17 18 
 export(getCompartments)
18 19 
 export(getDiamondInsulation)
19 20 
 export(localDistanceLaw)
... ... 
@@ -29,7 +30,6 @@ import(InteractionSet)
29 30 
 import(stringr)
30 31 
 import(tibble)
31 32 
 import(tidyr)
32 
-importClassesFrom(GenomicRanges,GRanges)
33 33 
 importFrom(BiocIO,import)
34 34 
 importFrom(BiocParallel,bplapply)
35 35 
 importFrom(BiocParallel,bpparam)
Browse code

minor fixes

js2264 authored on 01/01/2023 22:50:24
Showing 1 changed files
NAMESPACE
History View file @ 2e78ad1
... ... 
@@ -14,6 +14,8 @@ export(detrend)
14 14 
 export(distanceLaw)
15 15 
 export(divide)
16 16 
 export(full_contacts_yeast)
17 
+export(getCompartments)
18 
+export(getDiamondInsulation)
17 19 
 export(localDistanceLaw)
18 20 
 export(merge)
19 21 
 export(plot4C)
... ... 
@@ -29,6 +31,8 @@ import(tibble)
29 31 
 import(tidyr)
30 32 
 importClassesFrom(GenomicRanges,GRanges)
31 33 
 importFrom(BiocIO,import)
34 
+importFrom(BiocParallel,bplapply)
35 
+importFrom(BiocParallel,bpparam)
32 36 
 importFrom(GenomicRanges,GRanges)
33 37 
 importFrom(GenomicRanges,end)
34 38 
 importFrom(GenomicRanges,findOverlaps)
... ... 
@@ -39,11 +43,13 @@ importFrom(InteractionSet,GInteractions)
39 43 
 importFrom(InteractionSet,anchors)
40 44 
 importFrom(InteractionSet,pairdist)
41 45 
 importFrom(InteractionSet,regions)
46 
+importFrom(Matrix,sparseMatrix)
42 47 
 importFrom(RSpectra,eigs_sym)
43 48 
 importFrom(S4Vectors,SimpleList)
44 49 
 importFrom(S4Vectors,aggregate)
45 50 
 importFrom(S4Vectors,metadata)
46 51 
 importFrom(S4Vectors,queryHits)
52 
+importFrom(WGCNA,cor)
47 53 
 importFrom(dplyr,arrange)
48 54 
 importFrom(dplyr,bind_rows)
49 55 
 importFrom(dplyr,cur_data)
Browse code

convert plotMatrix to methods (HiCExperiment, GInteractions, matrix)

js2264 authored on 28/12/2022 23:20:08
Showing 1 changed files
NAMESPACE
History View file @ b67e5c9
... ... 
@@ -17,11 +17,11 @@ export(full_contacts_yeast)
17 17 
 export(localDistanceLaw)
18 18 
 export(merge)
19 19 
 export(plot4C)
20 
-export(plotMatrix)
21 20 
 export(plotPs)
22 21 
 export(plotPsSlope)
23 22 
 export(virtual4C)
24 23 
 exportMethods(aggregate)
24 
+exportMethods(plotMatrix)
25 25 
 import(HiCExperiment)
26 26 
 import(InteractionSet)
27 27 
 import(stringr)
Browse code

add aggregate method

js2264 authored on 26/12/2022 23:08:49
Showing 1 changed files
NAMESPACE
History View file @ 7505653
... ... 
@@ -21,6 +21,7 @@ export(plotMatrix)
21 21 
 export(plotPs)
22 22 
 export(plotPsSlope)
23 23 
 export(virtual4C)
24 
+exportMethods(aggregate)
24 25 
 import(HiCExperiment)
25 26 
 import(InteractionSet)
26 27 
 import(stringr)
... ... 
@@ -40,6 +41,7 @@ importFrom(InteractionSet,pairdist)
40 41 
 importFrom(InteractionSet,regions)
41 42 
 importFrom(RSpectra,eigs_sym)
42 43 
 importFrom(S4Vectors,SimpleList)
44 
+importFrom(S4Vectors,aggregate)
43 45 
 importFrom(S4Vectors,metadata)
44 46 
 importFrom(S4Vectors,queryHits)
45 47 
 importFrom(dplyr,arrange)
Browse code

add diamond insulation score and border annotation

js2264 authored on 23/12/2022 01:27:07
Showing 1 changed files
NAMESPACE
History View file @ 4c45dc3
... ... 
@@ -9,6 +9,7 @@ export(bwrColors)
9 9 
 export(cisTransRatio)
10 10 
 export(contacts_yeast)
11 11 
 export(contacts_yeast_eco1)
12 
+export(coolerColors)
12 13 
 export(detrend)
13 14 
 export(distanceLaw)
14 15 
 export(divide)
Browse code

add compartment annotation

js2264 authored on 19/12/2022 17:38:56
Showing 1 changed files
NAMESPACE
History View file @ 67118d2
... ... 
@@ -4,6 +4,7 @@ export(Contacts)
4 4 
 export(afmhotrColors)
5 5 
 export(autocorrelate)
6 6 
 export(bbrColors)
7 
+export(bgrColors)
7 8 
 export(bwrColors)
8 9 
 export(cisTransRatio)
9 10 
 export(contacts_yeast)
... ... 
@@ -36,6 +37,7 @@ importFrom(InteractionSet,GInteractions)
36 37 
 importFrom(InteractionSet,anchors)
37 38 
 importFrom(InteractionSet,pairdist)
38 39 
 importFrom(InteractionSet,regions)
40 
+importFrom(RSpectra,eigs_sym)
39 41 
 importFrom(S4Vectors,SimpleList)
40 42 
 importFrom(S4Vectors,metadata)
41 43 
 importFrom(S4Vectors,queryHits)
Browse code

minor fixes

js2264 authored on 13/12/2022 12:27:51
Showing 1 changed files
NAMESPACE
History View file @ e5b859f
... ... 
@@ -19,19 +19,18 @@ export(plotMatrix)
19 19 
 export(plotPs)
20 20 
 export(plotPsSlope)
21 21 
 export(virtual4C)
22 
-import(GenomicRanges)
23 22 
 import(HiCExperiment)
24 23 
 import(InteractionSet)
25 24 
 import(stringr)
26 25 
 import(tibble)
27 26 
 import(tidyr)
27 
+importClassesFrom(GenomicRanges,GRanges)
28 28 
 importFrom(BiocIO,import)
29 29 
 importFrom(GenomicRanges,GRanges)
30 30 
 importFrom(GenomicRanges,end)
31 31 
 importFrom(GenomicRanges,findOverlaps)
32 32 
 importFrom(GenomicRanges,seqnames)
33 33 
 importFrom(GenomicRanges,start)
34 
-importFrom(HiContactsData,HiContactsData)
35 34 
 importFrom(IRanges,IRanges)
36 35 
 importFrom(InteractionSet,GInteractions)
37 36 
 importFrom(InteractionSet,anchors)
Browse code

remove unnecessary deps

js2264 authored on 23/11/2022 15:02:38
Showing 1 changed files
NAMESPACE
History View file @ 5840cf2
... ... 
@@ -25,6 +25,7 @@ import(InteractionSet)
25 25 
 import(stringr)
26 26 
 import(tibble)
27 27 
 import(tidyr)
28 
+importFrom(BiocIO,import)
28 29 
 importFrom(GenomicRanges,GRanges)
29 30 
 importFrom(GenomicRanges,end)
30 31 
 importFrom(GenomicRanges,findOverlaps)
Browse code

v. 1.1.1: move classes and methods to HiCExperiment package

js2264 authored on 20/11/2022 22:10:18
Showing 1 changed files
NAMESPACE
History View file @ 5ae528d
... ... 
@@ -12,81 +12,33 @@ export(detrend)
12 12 
 export(distanceLaw)
13 13 
 export(divide)
14 14 
 export(full_contacts_yeast)
15 
-export(is_symmetrical)
16 15 
 export(localDistanceLaw)
17 
-export(lsCoolResolutions)
18 16 
 export(merge)
19 
-export(pairs2gi)
20 17 
 export(plot4C)
21 18 
 export(plotMatrix)
22 19 
 export(plotPs)
23 20 
 export(plotPsSlope)
24 
-export(setAs)
25 21 
 export(virtual4C)
26 
-exportClasses(Contacts)
27 
-exportMethods("[")
28 
-exportMethods("focus<-")
29 
-exportMethods("interactions<-")
30 
-exportMethods("metadata<-")
31 
-exportMethods("pairsFile<-")
32 
-exportMethods("scores<-")
33 
-exportMethods("topologicalFeatures<-")
34 
-exportMethods(anchors)
35 
-exportMethods(bins)
36 
-exportMethods(fileName)
37 
-exportMethods(focus)
38 
-exportMethods(interactions)
39 
-exportMethods(length)
40 
-exportMethods(pairsFile)
41 
-exportMethods(regions)
42 
-exportMethods(resolution)
43 
-exportMethods(resolutions)
44 
-exportMethods(scores)
45 
-exportMethods(seqinfo)
46 
-exportMethods(show)
47 
-exportMethods(summary)
48 
-exportMethods(topologicalFeatures)
49 
-import(GenomicInteractions)
50 22 
 import(GenomicRanges)
23 
+import(HiCExperiment)
51 24 
 import(InteractionSet)
52 
-import(ggplot2)
53 
-import(methods)
54 
-import(reticulate)
55 
-import(rhdf5)
56 25 
 import(stringr)
57 26 
 import(tibble)
58 27 
 import(tidyr)
59 
-importClassesFrom(S4Vectors,Annotated)
60 
-importClassesFrom(S4Vectors,Pairs)
61 
-importFrom(GenomeInfoDb,Seqinfo)
62 
-importFrom(GenomeInfoDb,seqlengths)
63 
-importFrom(GenomicInteractions,GenomicInteractions)
64 
-importFrom(GenomicInteractions,calculateDistances)
65 28 
 importFrom(GenomicRanges,GRanges)
66 
-importFrom(GenomicRanges,GRangesList)
67 29 
 importFrom(GenomicRanges,end)
68 30 
 importFrom(GenomicRanges,findOverlaps)
69 
-importFrom(GenomicRanges,mcols)
70 
-importFrom(GenomicRanges,resize)
71 31 
 importFrom(GenomicRanges,seqnames)
72 32 
 importFrom(GenomicRanges,start)
73 33 
 importFrom(HiContactsData,HiContactsData)
74 34 
 importFrom(IRanges,IRanges)
75 
-importFrom(IRanges,subsetByOverlaps)
76 35 
 importFrom(InteractionSet,GInteractions)
77 36 
 importFrom(InteractionSet,anchors)
78 37 
 importFrom(InteractionSet,pairdist)
79 
-importFrom(InteractionSet,reduceRegions)
80 38 
 importFrom(InteractionSet,regions)
81 
-importFrom(Matrix,as.matrix)
82 
-importFrom(Matrix,head)
83 
-importFrom(S4Vectors,Pairs)
84 39 
 importFrom(S4Vectors,SimpleList)
85 40 
 importFrom(S4Vectors,metadata)
86 41 
 importFrom(S4Vectors,queryHits)
87 
-importFrom(S4Vectors,subjectHits)
88 
-importFrom(S4Vectors,zipdown)
89 
-importFrom(S4Vectors,zipup)
90 42 
 importFrom(dplyr,arrange)
91 43 
 importFrom(dplyr,bind_rows)
92 44 
 importFrom(dplyr,cur_data)
... ... 
@@ -107,18 +59,12 @@ importFrom(dplyr,slice_max)
107 59 
 importFrom(dplyr,summarize)
108 60 
 importFrom(dplyr,tally)
109 61 
 importFrom(ggrastr,geom_tile_rast)
110 
-importFrom(glue,glue)
111 
-importFrom(methods,is)
112 
-importFrom(methods,setClass)
113 62 
 importFrom(scales,oob_squish)
114 63 
 importFrom(scales,rescale)
115 64 
 importFrom(scales,trans_breaks)
116 65 
 importFrom(scales,trans_format)
117 66 
 importFrom(scales,unit_format)
118 
-importFrom(stringr,str_split)
119 67 
 importFrom(tibble,as_tibble)
120 68 
 importFrom(tibble,tibble)
121 69 
 importFrom(tidyr,pivot_longer)
122 70 
 importFrom(tidyr,pivot_wider)
123 
-importFrom(vroom,vroom)
124 
-importMethodsFrom(BiocGenerics,fileName)
Browse code

replace data.table::fread by vroom::vroom

js2264 authored on 12/10/2022 20:51:33
Showing 1 changed files
NAMESPACE
History View file @ 08acbbe
... ... 
@@ -87,7 +87,6 @@ importFrom(S4Vectors,queryHits)
87 87 
 importFrom(S4Vectors,subjectHits)
88 88 
 importFrom(S4Vectors,zipdown)
89 89 
 importFrom(S4Vectors,zipup)
90 
-importFrom(data.table,fread)
91 90 
 importFrom(dplyr,arrange)
92 91 
 importFrom(dplyr,bind_rows)
93 92 
 importFrom(dplyr,cur_data)
... ... 
@@ -121,4 +120,5 @@ importFrom(tibble,as_tibble)
121 120 
 importFrom(tibble,tibble)
122 121 
 importFrom(tidyr,pivot_longer)
123 122 
 importFrom(tidyr,pivot_wider)
123 
+importFrom(vroom,vroom)
124 124 
 importMethodsFrom(BiocGenerics,fileName)
Browse code

Cleanup methods

js2264 authored on 22/09/2022 21:19:26
Showing 1 changed files
NAMESPACE
History View file @ b283b0e
... ... 
@@ -1,15 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("focus<-")
4 
-export("metadata<-")
5 
-export("pairsFile<-")
6 
-export("scores<-")
7 
-export("topologicalFeatures<-")
8 3 
 export(Contacts)
9 4 
 export(afmhotrColors)
10 5 
 export(autocorrelate)
11 6 
 export(bbrColors)
12 
-export(bins)
13 7 
 export(bwrColors)
14 8 
 export(cisTransRatio)
15 9 
 export(contacts_yeast)
... ... 
@@ -17,35 +11,41 @@ export(contacts_yeast_eco1)
17 11 
 export(detrend)
18 12 
 export(distanceLaw)
19 13 
 export(divide)
20 
-export(focus)
21 14 
 export(full_contacts_yeast)
22 15 
 export(is_symmetrical)
23 16 
 export(localDistanceLaw)
24 17 
 export(lsCoolResolutions)
25 18 
 export(merge)
26 19 
 export(pairs2gi)
27 
-export(pairsFile)
28 20 
 export(plot4C)
29 21 
 export(plotMatrix)
30 22 
 export(plotPs)
31 23 
 export(plotPsSlope)
32 
-export(resolutions)
33 
-export(scores)
34 24 
 export(setAs)
35 
-export(topologicalFeatures)
36 25 
 export(virtual4C)
37 26 
 exportClasses(Contacts)
38 27 
 exportMethods("[")
28 
+exportMethods("focus<-")
39 29 
 exportMethods("interactions<-")
30 
+exportMethods("metadata<-")
31 
+exportMethods("pairsFile<-")
32 
+exportMethods("scores<-")
33 
+exportMethods("topologicalFeatures<-")
40 34 
 exportMethods(anchors)
35 
+exportMethods(bins)
41 36 
 exportMethods(fileName)
37 
+exportMethods(focus)
42 38 
 exportMethods(interactions)
43 39 
 exportMethods(length)
40 
+exportMethods(pairsFile)
44 41 
 exportMethods(regions)
45 42 
 exportMethods(resolution)
43 
+exportMethods(resolutions)
44 
+exportMethods(scores)
46 45 
 exportMethods(seqinfo)
47 46 
 exportMethods(show)
48 47 
 exportMethods(summary)
48 
+exportMethods(topologicalFeatures)
49 49 
 import(GenomicInteractions)
50 50 
 import(GenomicRanges)
51 51 
 import(InteractionSet)
Browse code

ignore APA for now

js2264 authored on 22/09/2022 06:59:46
Showing 1 changed files
NAMESPACE
History View file @ a111f48
... ... 
@@ -20,6 +20,7 @@ export(divide)
20 20 
 export(focus)
21 21 
 export(full_contacts_yeast)
22 22 
 export(is_symmetrical)
23 
+export(localDistanceLaw)
23 24 
 export(lsCoolResolutions)
24 25 
 export(merge)
25 26 
 export(pairs2gi)
... ... 
@@ -59,7 +60,6 @@ importClassesFrom(S4Vectors,Annotated)
59 60 
 importClassesFrom(S4Vectors,Pairs)
60 61 
 importFrom(GenomeInfoDb,Seqinfo)
61 62 
 importFrom(GenomeInfoDb,seqlengths)
62 
-importFrom(GenomeInfoDb,seqnames)
63 63 
 importFrom(GenomicInteractions,GenomicInteractions)
64 64 
 importFrom(GenomicInteractions,calculateDistances)
65 65 
 importFrom(GenomicRanges,GRanges)
... ... 
@@ -67,11 +67,9 @@ importFrom(GenomicRanges,GRangesList)
67 67 
 importFrom(GenomicRanges,end)
68 68 
 importFrom(GenomicRanges,findOverlaps)
69 69 
 importFrom(GenomicRanges,mcols)
70 
-importFrom(GenomicRanges,nearest)
71 70 
 importFrom(GenomicRanges,resize)
72 71 
 importFrom(GenomicRanges,seqnames)
73 72 
 importFrom(GenomicRanges,start)
74 
-importFrom(GenomicRanges,width)
75 73 
 importFrom(HiContactsData,HiContactsData)
76 74 
 importFrom(IRanges,IRanges)
77 75 
 importFrom(IRanges,subsetByOverlaps)
... ... 
@@ -111,7 +109,6 @@ importFrom(dplyr,summarize)
111 109 
 importFrom(dplyr,tally)
112 110 
 importFrom(ggrastr,geom_tile_rast)
113 111 
 importFrom(glue,glue)
114 
-importFrom(methods,as)
115 112 
 importFrom(methods,is)
116 113 
 importFrom(methods,setClass)
117 114 
 importFrom(scales,oob_squish)
Browse code

`contacts` class/function renamed to `Contacts`

js2264 authored on 22/09/2022 06:57:42
Showing 1 changed files
NAMESPACE
History View file @ 3d6f9b1
... ... 
@@ -5,13 +5,13 @@ export("metadata<-")
5 5 
 export("pairsFile<-")
6 6 
 export("scores<-")
7 7 
 export("topologicalFeatures<-")
8 
+export(Contacts)
8 9 
 export(afmhotrColors)
9 10 
 export(autocorrelate)
10 11 
 export(bbrColors)
11 12 
 export(bins)
12 13 
 export(bwrColors)
13 14 
 export(cisTransRatio)
14 
-export(contacts)
15 15 
 export(contacts_yeast)
16 16 
 export(contacts_yeast_eco1)
17 17 
 export(detrend)
... ... 
@@ -33,7 +33,7 @@ export(scores)
33 33 
 export(setAs)
34 34 
 export(topologicalFeatures)
35 35 
 export(virtual4C)
36 
-exportClasses(contacts)
36 
+exportClasses(Contacts)
37 37 
 exportMethods("[")
38 38 
 exportMethods("interactions<-")
39 39 
 exportMethods(anchors)
Browse code

rename getPs -> distanceLaw

js2264 authored on 22/09/2022 06:32:36
Showing 1 changed files
NAMESPACE
History View file @ 556f51a
... ... 
@@ -15,10 +15,10 @@ export(contacts)
15 15 
 export(contacts_yeast)
16 16 
 export(contacts_yeast_eco1)
17 17 
 export(detrend)
18 
+export(distanceLaw)
18 19 
 export(divide)
19 20 
 export(focus)
20 21 
 export(full_contacts_yeast)
21 
-export(getPs)
22 22 
 export(is_symmetrical)
23 23 
 export(lsCoolResolutions)
24 24 
 export(merge)
Browse code

rename functions

js2264 authored on 22/09/2022 06:30:19
Showing 1 changed files
NAMESPACE
History View file @ 6e6273d
... ... 
@@ -1,5 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export("focus<-")
3 4 
 export("metadata<-")
4 5 
 export("pairsFile<-")
5 6 
 export("scores<-")
Browse code

simulateBorders and start of APA refactoring

js2264 authored on 20/09/2022 21:44:55
Showing 1 changed files
NAMESPACE
History View file @ 524ba43
... ... 
@@ -58,6 +58,7 @@ importClassesFrom(S4Vectors,Annotated)
58 58 
 importClassesFrom(S4Vectors,Pairs)
59 59 
 importFrom(GenomeInfoDb,Seqinfo)
60 60 
 importFrom(GenomeInfoDb,seqlengths)
61 
+importFrom(GenomeInfoDb,seqnames)
61 62 
 importFrom(GenomicInteractions,GenomicInteractions)
62 63 
 importFrom(GenomicInteractions,calculateDistances)
63 64 
 importFrom(GenomicRanges,GRanges)
... ... 
@@ -65,15 +66,18 @@ importFrom(GenomicRanges,GRangesList)
65 66 
 importFrom(GenomicRanges,end)
66 67 
 importFrom(GenomicRanges,findOverlaps)
67 68 
 importFrom(GenomicRanges,mcols)
69 
+importFrom(GenomicRanges,nearest)
68 70 
 importFrom(GenomicRanges,resize)
69 71 
 importFrom(GenomicRanges,seqnames)
70 72 
 importFrom(GenomicRanges,start)
73 
+importFrom(GenomicRanges,width)
71 74 
 importFrom(HiContactsData,HiContactsData)
72 75 
 importFrom(IRanges,IRanges)
73 76 
 importFrom(IRanges,subsetByOverlaps)
74 77 
 importFrom(InteractionSet,GInteractions)
75 78 
 importFrom(InteractionSet,anchors)
76 79 
 importFrom(InteractionSet,pairdist)
80 
+importFrom(InteractionSet,reduceRegions)
77 81 
 importFrom(InteractionSet,regions)
78 82 
 importFrom(Matrix,as.matrix)
79 83 
 importFrom(Matrix,head)
... ... 
@@ -106,6 +110,7 @@ importFrom(dplyr,summarize)
106 110 
 importFrom(dplyr,tally)
107 111 
 importFrom(ggrastr,geom_tile_rast)
108 112 
 importFrom(glue,glue)
113 
+importFrom(methods,as)
109 114 
 importFrom(methods,is)
110 115 
 importFrom(methods,setClass)
111 116 
 importFrom(scales,oob_squish)
Browse code

tyding up methods

js2264 authored on 20/09/2022 11:38:58
Showing 1 changed files
NAMESPACE
History View file @ 1fb27b7
... ... 
@@ -1,5 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export("metadata<-")
3 4 
 export("pairsFile<-")
4 5 
 export("scores<-")
5 6 
 export("topologicalFeatures<-")
Browse code

renamed slots to fileName & pairsFile

js2264 authored on 20/09/2022 11:24:06
Showing 1 changed files
NAMESPACE
History View file @ 99a099a
... ... 
@@ -12,7 +12,6 @@ export(cisTransRatio)
12 12 
 export(contacts)
13 13 
 export(contacts_yeast)
14 14 
 export(contacts_yeast_eco1)
15 
-export(coolPath)
16 15 
 export(detrend)
17 16 
 export(divide)
18 17 
 export(focus)
... ... 
@@ -36,6 +35,7 @@ exportClasses(contacts)
36 35 
 exportMethods("[")
37 36 
 exportMethods("interactions<-")
38 37 
 exportMethods(anchors)
38 
+exportMethods(fileName)
39 39 
 exportMethods(interactions)
40 40 
 exportMethods(length)
41 41 
 exportMethods(regions)
... ... 
@@ -117,3 +117,4 @@ importFrom(tibble,as_tibble)
117 117 
 importFrom(tibble,tibble)
118 118 
 importFrom(tidyr,pivot_longer)
119 119 
 importFrom(tidyr,pivot_wider)
120 
+importMethodsFrom(BiocGenerics,fileName)
Browse code

dropped useless slots (bins, seqinfo and matrixType) and replace by on-the-fly generating functions

js2264 authored on 20/09/2022 10:49:33
Showing 1 changed files
NAMESPACE
History View file @ 7e7a38e
... ... 
@@ -1,6 +1,5 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("matrixType<-")
4 3 
 export("pairsFile<-")
5 4 
 export("scores<-")
6 5 
 export("topologicalFeatures<-")
... ... 
@@ -21,7 +20,6 @@ export(full_contacts_yeast)
21 20 
 export(getPs)
22 21 
 export(is_symmetrical)
23 22 
 export(lsCoolResolutions)
24 
-export(matrixType)
25 23 
 export(merge)
26 24 
 export(pairs2gi)
27 25 
 export(pairsFile)
Browse code

update doc

js2264 authored on 20/09/2022 10:07:50
Showing 1 changed files
NAMESPACE
History View file @ c735c62
... ... 
@@ -1,9 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("features<-")
4 3 
 export("matrixType<-")
5 4 
 export("pairsFile<-")
6 5 
 export("scores<-")
6 
+export("topologicalFeatures<-")
7 7 
 export(afmhotrColors)
8 8 
 export(autocorrelate)
9 9 
 export(bbrColors)
... ... 
@@ -12,11 +12,12 @@ export(bwrColors)
12 12 
 export(cisTransRatio)
13 13 
 export(contacts)
14 14 
 export(contacts_yeast)
15 
+export(contacts_yeast_eco1)
15 16 
 export(coolPath)
16 17 
 export(detrend)
17 18 
 export(divide)
18 
-export(features)
19 19 
 export(focus)
20 
+export(full_contacts_yeast)
20 21 
 export(getPs)
21 22 
 export(is_symmetrical)
22 23 
 export(lsCoolResolutions)
... ... 
@@ -31,6 +32,7 @@ export(plotPsSlope)
31 32 
 export(resolutions)
32 33 
 export(scores)
33 34 
 export(setAs)
35 
+export(topologicalFeatures)
34 36 
 export(virtual4C)
35 37 
 exportClasses(contacts)
36 38 
 exportMethods("[")
Browse code

replace data files by import functions

js2264 authored on 20/09/2022 08:22:08
Showing 1 changed files
NAMESPACE
History View file @ d59541b
... ... 
@@ -11,6 +11,7 @@ export(bins)
11 11 
 export(bwrColors)
12 12 
 export(cisTransRatio)
13 13 
 export(contacts)
14 
+export(contacts_yeast)
14 15 
 export(coolPath)
15 16 
 export(detrend)
16 17 
 export(divide)
... ... 
@@ -66,6 +67,7 @@ importFrom(GenomicRanges,mcols)
66 67 
 importFrom(GenomicRanges,resize)
67 68 
 importFrom(GenomicRanges,seqnames)
68 69 
 importFrom(GenomicRanges,start)
70 
+importFrom(HiContactsData,HiContactsData)
69 71 
 importFrom(IRanges,IRanges)
70 72 
 importFrom(IRanges,subsetByOverlaps)
71 73 
 importFrom(InteractionSet,GInteractions)
Browse code

update README

js2264 authored on 19/09/2022 17:42:57
Showing 1 changed files
NAMESPACE
History View file @ b7824cc
... ... 
@@ -29,6 +29,7 @@ export(plotPs)
29 29 
 export(plotPsSlope)
30 30 
 export(resolutions)
31 31 
 export(scores)
32 
+export(setAs)
32 33 
 export(virtual4C)
33 34 
 exportClasses(contacts)
34 35 
 exportMethods("[")
... ... 
@@ -83,6 +84,7 @@ importFrom(S4Vectors,zipup)
83 84 
 importFrom(data.table,fread)
84 85 
 importFrom(dplyr,arrange)
85 86 
 importFrom(dplyr,bind_rows)
87 
+importFrom(dplyr,cur_data)
86 88 
 importFrom(dplyr,distinct)
87 89 
 importFrom(dplyr,filter)
88 90 
 importFrom(dplyr,group_by)
... ... 
@@ -90,6 +92,7 @@ importFrom(dplyr,group_split)
90 92 
 importFrom(dplyr,lead)
91 93 
 importFrom(dplyr,left_join)
92 94 
 importFrom(dplyr,mutate)
95 
+importFrom(dplyr,n)
93 96 
 importFrom(dplyr,pull)
94 97 
 importFrom(dplyr,relocate)
95 98 
 importFrom(dplyr,rename)
Browse code

update doc

js2264 authored on 19/09/2022 15:33:46
Showing 1 changed files
NAMESPACE
History View file @ 9ed8429
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export("features<-")
4 
+export("matrixType<-")
4 5 
 export("pairsFile<-")
5 6 
 export("scores<-")
6 7 
 export(afmhotrColors)
... ... 
@@ -31,6 +32,7 @@ export(scores)
31 32 
 export(virtual4C)
32 33 
 exportClasses(contacts)
33 34 
 exportMethods("[")
35 
+exportMethods("interactions<-")
34 36 
 exportMethods(anchors)
35 37 
 exportMethods(interactions)
36 38 
 exportMethods(length)
Browse code

remove APA/scalogram functions

js2264 authored on 18/09/2022 18:30:38
Showing 1 changed files
NAMESPACE
History View file @ 702819c
... ... 
@@ -43,7 +43,6 @@ import(GenomicInteractions)
43 43 
 import(GenomicRanges)
44 44 
 import(InteractionSet)
45 45 
 import(ggplot2)
46 
-import(ggrastr)
47 46 
 import(methods)
48 47 
 import(reticulate)
49 48 
 import(rhdf5)
... ... 
@@ -54,7 +53,6 @@ importClassesFrom(S4Vectors,Annotated)
54 53 
 importClassesFrom(S4Vectors,Pairs)
55 54 
 importFrom(GenomeInfoDb,Seqinfo)
56 55 
 importFrom(GenomeInfoDb,seqlengths)
57 
-importFrom(GenomeInfoDb,seqnames)
58 56 
 importFrom(GenomicInteractions,GenomicInteractions)
59 57 
 importFrom(GenomicInteractions,calculateDistances)
60 58 
 importFrom(GenomicRanges,GRanges)
... ... 
@@ -62,11 +60,9 @@ importFrom(GenomicRanges,GRangesList)
62 60 
 importFrom(GenomicRanges,end)
63 61 
 importFrom(GenomicRanges,findOverlaps)
64 62 
 importFrom(GenomicRanges,mcols)
65 
-importFrom(GenomicRanges,nearest)
66 63 
 importFrom(GenomicRanges,resize)
67 64 
 importFrom(GenomicRanges,seqnames)
68 65 
 importFrom(GenomicRanges,start)
69 
-importFrom(GenomicRanges,width)
70 66 
 importFrom(IRanges,IRanges)
71 67 
 importFrom(IRanges,subsetByOverlaps)
72 68 
 importFrom(InteractionSet,GInteractions)
... ... 
@@ -88,7 +84,6 @@ importFrom(dplyr,bind_rows)
88 84 
 importFrom(dplyr,distinct)
89 85 
 importFrom(dplyr,filter)
90 86 
 importFrom(dplyr,group_by)
91 
-importFrom(dplyr,group_modify)
92 87 
 importFrom(dplyr,group_split)
93 88 
 importFrom(dplyr,lead)
94 89 
 importFrom(dplyr,left_join)
... ... 
@@ -103,7 +98,6 @@ importFrom(dplyr,summarize)
103 98 
 importFrom(dplyr,tally)
104 99 
 importFrom(ggrastr,geom_tile_rast)
105 100 
 importFrom(glue,glue)
106 
-importFrom(methods,as)
107 101 
 importFrom(methods,is)
108 102 
 importFrom(methods,setClass)
109 103 
 importFrom(scales,oob_squish)
Browse code

update doc

js2264 authored on 18/09/2022 18:26:32
Showing 1 changed files
NAMESPACE
History View file @ be7b423
... ... 
@@ -15,7 +15,6 @@ export(detrend)
15 15 
 export(divide)
16 16 
 export(features)
17 17 
 export(focus)
18 
-export(getHicStats)
19 18 
 export(getPs)
20 19 
 export(is_symmetrical)
21 20 
 export(lsCoolResolutions)
Browse code

Add matrixType and coolPath

js2264 authored on 18/09/2022 11:18:36
Showing 1 changed files
NAMESPACE
History View file @ 9675463
... ... 
@@ -19,6 +19,7 @@ export(getHicStats)
19 19 
 export(getPs)
20 20 
 export(is_symmetrical)
21 21 
 export(lsCoolResolutions)
22 
+export(matrixType)
22 23 
 export(merge)
23 24 
 export(pairs2gi)
24 25 
 export(pairsFile)
... ... 
@@ -29,6 +30,7 @@ export(plotPsSlope)
29 30 
 export(resolutions)
30 31 
 export(scores)
31 32 
 export(virtual4C)
33 
+exportClasses(contacts)
32 34 
 exportMethods("[")
33 35 
 exportMethods(anchors)
34 36 
 exportMethods(interactions)
Browse code

update DESCRIPTION/NAMESPACE

js2264 authored on 18/09/2022 09:52:17
Showing 1 changed files
NAMESPACE
History View file @ a97560d
... ... 
@@ -3,16 +3,18 @@
3 3 
 export("features<-")
4 4 
 export("pairsFile<-")
5 5 
 export("scores<-")
6 
-export(.summary)
7 
-export(afmhotr_colors)
6 
+export(afmhotrColors)
8 7 
 export(autocorrelate)
9 
-export(bbr_colors)
10 
-export(bwr_colors)
11 
-export(cis_trans)
8 
+export(bbrColors)
9 
+export(bins)
10 
+export(bwrColors)
11 
+export(cisTransRatio)
12 12 
 export(contacts)
13 
+export(coolPath)
13 14 
 export(detrend)
14 15 
 export(divide)
15 16 
 export(features)
17 
+export(focus)
16 18 
 export(getHicStats)
17 19 
 export(getPs)
18 20 
 export(is_symmetrical)
... ... 
@@ -24,29 +26,29 @@ export(plot4C)
24 26 
 export(plotMatrix)
25 27 
 export(plotPs)
26 28 
 export(plotPsSlope)
29 
+export(resolutions)
27 30 
 export(scores)
28 31 
 export(virtual4C)
29 32 
 exportMethods("[")
30 33 
 exportMethods(anchors)
34 
+exportMethods(interactions)
31 35 
 exportMethods(length)
32 36 
 exportMethods(regions)
37 
+exportMethods(resolution)
38 
+exportMethods(seqinfo)
33 39 
 exportMethods(show)
34 
-import(BiocParallel)
40 
+exportMethods(summary)
35 41 
 import(GenomicInteractions)
36 42 
 import(GenomicRanges)
37 
-import(HiContactsData)
38 43 
 import(InteractionSet)
39 44 
 import(ggplot2)
40 45 
 import(ggrastr)
41 46 
 import(methods)
42 
-import(plyranges)
43 47 
 import(reticulate)
44 48 
 import(rhdf5)
45 49 
 import(stringr)
46 50 
 import(tibble)
47 51 
 import(tidyr)
48 
-import(tools)
49 
-import(zeallot)
50 52 
 importClassesFrom(S4Vectors,Annotated)
51 53 
 importClassesFrom(S4Vectors,Pairs)
52 54 
 importFrom(GenomeInfoDb,Seqinfo)
... ... 
@@ -79,7 +81,6 @@ importFrom(S4Vectors,queryHits)
79 81 
 importFrom(S4Vectors,subjectHits)
80 82 
 importFrom(S4Vectors,zipdown)
81 83 
 importFrom(S4Vectors,zipup)
82 
-importFrom(corrr,correlate)
83 84 
 importFrom(data.table,fread)
84 85 
 importFrom(dplyr,arrange)
85 86 
 importFrom(dplyr,bind_rows)
Browse code

fix is_centered and rename to is_symmetrical

js2264 authored on 16/09/2022 12:45:38
Showing 1 changed files
NAMESPACE
History View file @ 82ac56e
... ... 
@@ -15,6 +15,7 @@ export(divide)
15 15 
 export(features)
16 16 
 export(getHicStats)
17 17 
 export(getPs)
18 
+export(is_symmetrical)
18 19 
 export(lsCoolResolutions)
19 20 
 export(merge)
20 21 
 export(pairs2gi)
Browse code

remove unnecessary functions

js2264 authored on 15/09/2022 16:59:33
Showing 1 changed files
NAMESPACE
History View file @ ec4d54e
... ... 
@@ -27,7 +27,6 @@ export(scores)
27 27 
 export(virtual4C)
28 28 
 exportMethods("[")
29 29 
 exportMethods(anchors)
30 
-exportMethods(dim)
31 30 
 exportMethods(length)
32 31 
 exportMethods(regions)
33 32 
 exportMethods(show)
Browse code

remove APA from vignette for now

js2264 authored on 13/09/2022 08:21:46
Showing 1 changed files
NAMESPACE
History View file @ c2ce683
... ... 
@@ -3,6 +3,7 @@
3 3 
 export("features<-")
4 4 
 export("pairsFile<-")
5 5 
 export("scores<-")
6 
+export(.summary)
6 7 
 export(afmhotr_colors)
7 8 
 export(autocorrelate)
8 9 
 export(bbr_colors)
Browse code

fix minor bugs

js2264 authored on 08/09/2022 15:09:15
Showing 1 changed files
NAMESPACE
History View file @ a1f2497
... ... 
@@ -1,6 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("feature<-")
3 
+export("features<-")
4 4 
 export("pairsFile<-")
5 5 
 export("scores<-")
6 6 
 export(afmhotr_colors)
... ... 
@@ -11,10 +11,10 @@ export(cis_trans)
11 11 
 export(contacts)
12 12 
 export(detrend)
13 13 
 export(divide)
14 
-export(feature)
15 14 
 export(features)
16 15 
 export(getHicStats)
17 16 
 export(getPs)
17 
+export(lsCoolResolutions)
18 18 
 export(merge)
19 19 
 export(pairs2gi)
20 20 
 export(pairsFile)
Browse code

changed assay(s) to scores

js2264 authored on 31/08/2022 15:35:35
Showing 1 changed files
NAMESPACE
History View file @ 9cbab23
... ... 
@@ -1,11 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("assay<-")
4 3 
 export("feature<-")
5 4 
 export("pairsFile<-")
5 
+export("scores<-")
6 6 
 export(afmhotr_colors)
7 
-export(assay)
8 
-export(assays)
9 7 
 export(autocorrelate)
10 8 
 export(bbr_colors)
11 9 
 export(bwr_colors)
... ... 
@@ -24,6 +22,7 @@ export(plot4C)
24 22 
 export(plotMatrix)
25 23 
 export(plotPs)
26 24 
 export(plotPsSlope)
25 
+export(scores)
27 26 
 export(virtual4C)
28 27 
 exportMethods("[")
29 28 
 exportMethods(anchors)
Browse code

fix doc and examples

js2264 authored on 31/08/2022 15:12:40
Showing 1 changed files
NAMESPACE
History View file @ a599559
... ... 
@@ -1,22 +1,35 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export("assay<-")
4 
+export("feature<-")
5 
+export("pairsFile<-")
6 
+export(afmhotr_colors)
7 
+export(assay)
8 
+export(assays)
3 9 
 export(autocorrelate)
10 
+export(bbr_colors)
11 
+export(bwr_colors)
4 12 
 export(cis_trans)
5 13 
 export(contacts)
6 14 
 export(detrend)
7 15 
 export(divide)
16 
+export(feature)
17 
+export(features)
8 18 
 export(getHicStats)
9 19 
 export(getPs)
10 20 
 export(merge)
11 21 
 export(pairs2gi)
22 
+export(pairsFile)
12 23 
 export(plot4C)
13 24 
 export(plotMatrix)
14 25 
 export(plotPs)
15 26 
 export(plotPsSlope)
16 27 
 export(virtual4C)
17 28 
 exportMethods("[")
29 
+exportMethods(anchors)
18 30 
 exportMethods(dim)
19 31 
 exportMethods(length)
32 
+exportMethods(regions)
20 33 
 exportMethods(show)
21 34 
 import(BiocParallel)
22 35 
 import(GenomicInteractions)
... ... 
@@ -34,6 +47,7 @@ import(tibble)
34 47 
 import(tidyr)
35 48 
 import(tools)
36 49 
 import(zeallot)
50 
+importClassesFrom(S4Vectors,Annotated)
37 51 
 importClassesFrom(S4Vectors,Pairs)
38 52 
 importFrom(GenomeInfoDb,Seqinfo)
39 53 
 importFrom(GenomeInfoDb,seqlengths)
... ... 
@@ -89,6 +103,7 @@ importFrom(ggrastr,geom_tile_rast)
89 103 
 importFrom(glue,glue)
90 104 
 importFrom(methods,as)
91 105 
 importFrom(methods,is)
106 
+importFrom(methods,setClass)
92 107 
 importFrom(scales,oob_squish)
93 108 
 importFrom(scales,rescale)
94 109 
 importFrom(scales,trans_breaks)
Browse code

add test units

js2264 authored on 31/08/2022 10:39:57
Showing 1 changed files
NAMESPACE
History View file @ 5968a3a
... ... 
@@ -1,6 +1,5 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export(APA)
4 3 
 export(autocorrelate)
5 4 
 export(cis_trans)
6 5 
 export(contacts)
... ... 
@@ -8,16 +7,12 @@ export(detrend)
8 7 
 export(divide)
9 8 
 export(getHicStats)
10 9 
 export(getPs)
11 
-export(gg4C)
12 
-export(ggMatrix)
13 
-export(ggPs)
14 
-export(ggPsSlope)
15 
-export(ggtheme_HiContacts)
16 
-export(ggtheme_HiContacts_tracks)
17 10 
 export(merge)
18 11 
 export(pairs2gi)
12 
+export(plot4C)
19 13 
 export(plotMatrix)
20 
-export(smoothen)
14 
+export(plotPs)
15 
+export(plotPsSlope)
21 16 
 export(virtual4C)
22 17 
 exportMethods("[")
23 18 
 exportMethods(dim)
Browse code

update doc with rdname tags

js2264 authored on 30/08/2022 15:20:52
Showing 1 changed files
NAMESPACE
History View file @ 1a6cf3c
... ... 
@@ -1,39 +1,25 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(APA)
4 
-export(addFeature)
5 4 
 export(autocorrelate)
6 5 
 export(cis_trans)
7 6 
 export(contacts)
8 
-export(cool2gi)
9 
-export(cool2seqinfo)
10 7 
 export(detrend)
11 8 
 export(divide)
12 
-export(fetchCool)
13 
-export(formatCoords)
14 
-export(getAnchors)
15 
-export(getCounts)
16 9 
 export(getHicStats)
17 10 
 export(getPs)
18 
-export(getScalogram)
19 11 
 export(gg4C)
20 12 
 export(ggMatrix)
21 13 
 export(ggPs)
22 14 
 export(ggPsSlope)
23 
-export(ggScalogram)
24 15 
 export(ggtheme_HiContacts)
25 16 
 export(ggtheme_HiContacts_tracks)
26 
-export(gi2cm)
27 
-export(lsCoolFiles)
28 
-export(lsCoolResolutions)
29 17 
 export(merge)
30 18 
 export(pairs2gi)
31 
-export(peekCool)
32 19 
 export(plotMatrix)
33 20 
 export(smoothen)
34 
-export(splitCoords)
35 21 
 export(virtual4C)
36 
-export(zoom)
22 
+exportMethods("[")
37 23 
 exportMethods(dim)
38 24 
 exportMethods(length)
39 25 
 exportMethods(show)
... ... 
@@ -53,12 +39,14 @@ import(tibble)
53 39 
 import(tidyr)
54 40 
 import(tools)
55 41 
 import(zeallot)
42 
+importClassesFrom(S4Vectors,Pairs)
56 43 
 importFrom(GenomeInfoDb,Seqinfo)
57 44 
 importFrom(GenomeInfoDb,seqlengths)
58 45 
 importFrom(GenomeInfoDb,seqnames)
59 46 
 importFrom(GenomicInteractions,GenomicInteractions)
60 47 
 importFrom(GenomicInteractions,calculateDistances)
61 48 
 importFrom(GenomicRanges,GRanges)
49 
+importFrom(GenomicRanges,GRangesList)
62 50 
 importFrom(GenomicRanges,end)
63 51 
 importFrom(GenomicRanges,findOverlaps)
64 52 
 importFrom(GenomicRanges,mcols)
... ... 
@@ -73,16 +61,19 @@ importFrom(InteractionSet,GInteractions)
73 61 
 importFrom(InteractionSet,anchors)
74 62 
 importFrom(InteractionSet,pairdist)
75 63 
 importFrom(InteractionSet,regions)
64 
+importFrom(Matrix,as.matrix)
76 65 
 importFrom(Matrix,head)
66 
+importFrom(S4Vectors,Pairs)
77 67 
 importFrom(S4Vectors,SimpleList)
78 68 
 importFrom(S4Vectors,metadata)
79 69 
 importFrom(S4Vectors,queryHits)
80 70 
 importFrom(S4Vectors,subjectHits)
71 
+importFrom(S4Vectors,zipdown)
72 
+importFrom(S4Vectors,zipup)
81 73 
 importFrom(corrr,correlate)
82 74 
 importFrom(data.table,fread)
83 75 
 importFrom(dplyr,arrange)
84 76 
 importFrom(dplyr,bind_rows)
85 
-importFrom(dplyr,case_when)
86 77 
 importFrom(dplyr,distinct)
87 78 
 importFrom(dplyr,filter)
88 79 
 importFrom(dplyr,group_by)
... ... 
@@ -102,11 +93,13 @@ importFrom(dplyr,tally)
102 93 
 importFrom(ggrastr,geom_tile_rast)
103 94 
 importFrom(glue,glue)
104 95 
 importFrom(methods,as)
96 
+importFrom(methods,is)
105 97 
 importFrom(scales,oob_squish)
106 98 
 importFrom(scales,rescale)
107 99 
 importFrom(scales,trans_breaks)
108 100 
 importFrom(scales,trans_format)
109 101 
 importFrom(scales,unit_format)
102 
+importFrom(stringr,str_split)
110 103 
 importFrom(tibble,as_tibble)
111 104 
 importFrom(tibble,tibble)
112 105 
 importFrom(tidyr,pivot_longer)
Browse code

doc

js2264 authored on 18/08/2022 16:44:16
Showing 1 changed files
NAMESPACE
History View file @ 9c1845e
... ... 
@@ -1,36 +1,53 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(APA)
4 
+export(addFeature)
5 
+export(autocorrelate)
6 
+export(cis_trans)
4 7 
 export(contacts)
5 8 
 export(cool2gi)
6 9 
 export(cool2seqinfo)
7 10 
 export(detrend)
11 
+export(divide)
8 12 
 export(fetchCool)
9 13 
 export(formatCoords)
10 14 
 export(getAnchors)
11 15 
 export(getCounts)
12 16 
 export(getHicStats)
13 17 
 export(getPs)
18 
+export(getScalogram)
14 19 
 export(gg4C)
15 20 
 export(ggMatrix)
16 21 
 export(ggPs)
22 
+export(ggPsSlope)
23 
+export(ggScalogram)
17 24 
 export(ggtheme_HiContacts)
18 25 
 export(ggtheme_HiContacts_tracks)
19 26 
 export(gi2cm)
20 27 
 export(lsCoolFiles)
21 28 
 export(lsCoolResolutions)
29 
+export(merge)
22 30 
 export(pairs2gi)
23 31 
 export(peekCool)
24 32 
 export(plotMatrix)
33 
+export(smoothen)
25 34 
 export(splitCoords)
35 
+export(virtual4C)
26 36 
 export(zoom)
37 
+exportMethods(dim)
38 
+exportMethods(length)
39 
+exportMethods(show)
27 40 
 import(BiocParallel)
41 
+import(GenomicInteractions)
42 
+import(GenomicRanges)
43 
+import(HiContactsData)
28 44 
 import(InteractionSet)
29 
-import(dplyr)
30 45 
 import(ggplot2)
31 46 
 import(ggrastr)
47 
+import(methods)
48 
+import(plyranges)
49 
+import(reticulate)
32 50 
 import(rhdf5)
33 
-import(scales)
34 51 
 import(stringr)
35 52 
 import(tibble)
36 53 
 import(tidyr)
... ... 
@@ -38,16 +55,59 @@ import(tools)
38 55 
 import(zeallot)
39 56 
 importFrom(GenomeInfoDb,Seqinfo)
40 57 
 importFrom(GenomeInfoDb,seqlengths)
58 
+importFrom(GenomeInfoDb,seqnames)
59 
+importFrom(GenomicInteractions,GenomicInteractions)
60 
+importFrom(GenomicInteractions,calculateDistances)
41 61 
 importFrom(GenomicRanges,GRanges)
42 62 
 importFrom(GenomicRanges,end)
43 63 
 importFrom(GenomicRanges,findOverlaps)
44 64 
 importFrom(GenomicRanges,mcols)
65 
+importFrom(GenomicRanges,nearest)
45 66 
 importFrom(GenomicRanges,resize)
46 67 
 importFrom(GenomicRanges,seqnames)
47 68 
 importFrom(GenomicRanges,start)
48 69 
 importFrom(GenomicRanges,width)
49 70 
 importFrom(IRanges,IRanges)
71 
+importFrom(IRanges,subsetByOverlaps)
72 
+importFrom(InteractionSet,GInteractions)
73 
+importFrom(InteractionSet,anchors)
74 
+importFrom(InteractionSet,pairdist)
75 
+importFrom(InteractionSet,regions)
76 
+importFrom(Matrix,head)
77 
+importFrom(S4Vectors,SimpleList)
78 
+importFrom(S4Vectors,metadata)
79 
+importFrom(S4Vectors,queryHits)
50 80 
 importFrom(S4Vectors,subjectHits)
81 
+importFrom(corrr,correlate)
82 
+importFrom(data.table,fread)
83 
+importFrom(dplyr,arrange)
84 
+importFrom(dplyr,bind_rows)
85 
+importFrom(dplyr,case_when)
86 
+importFrom(dplyr,distinct)
87 
+importFrom(dplyr,filter)
88 
+importFrom(dplyr,group_by)
89 
+importFrom(dplyr,group_modify)
90 
+importFrom(dplyr,group_split)
91 
+importFrom(dplyr,lead)
92 
+importFrom(dplyr,left_join)
93 
+importFrom(dplyr,mutate)
94 
+importFrom(dplyr,pull)
95 
+importFrom(dplyr,relocate)
96 
+importFrom(dplyr,rename)
97 
+importFrom(dplyr,select)
98 
+importFrom(dplyr,slice)
99 
+importFrom(dplyr,slice_max)
100 
+importFrom(dplyr,summarize)
101 
+importFrom(dplyr,tally)
102 
+importFrom(ggrastr,geom_tile_rast)
51 103 
 importFrom(glue,glue)
104 
+importFrom(methods,as)
105 
+importFrom(scales,oob_squish)
52 106 
 importFrom(scales,rescale)
107 
+importFrom(scales,trans_breaks)
108 
+importFrom(scales,trans_format)
109 
+importFrom(scales,unit_format)
110 
+importFrom(tibble,as_tibble)
53 111 
 importFrom(tibble,tibble)
112 
+importFrom(tidyr,pivot_longer)
113 
+importFrom(tidyr,pivot_wider)
Browse code

feat: improve README & doc

js2264 authored on 11/08/2022 16:03:10
Showing 1 changed files
NAMESPACE
History View file @ 98b4a8d
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(APA)
4 
+export(contacts)
4 5 
 export(cool2gi)
5 6 
 export(cool2seqinfo)
6 7 
 export(detrend)
... ... 
@@ -10,6 +11,7 @@ export(getAnchors)
10 11 
 export(getCounts)
11 12 
 export(getHicStats)
12 13 
 export(getPs)
14 
+export(gg4C)
13 15 
 export(ggMatrix)
14 16 
 export(ggPs)
15 17 
 export(ggtheme_HiContacts)
... ... 
@@ -21,6 +23,7 @@ export(pairs2gi)
21 23 
 export(peekCool)
22 24 
 export(plotMatrix)
23 25 
 export(splitCoords)
26 
+export(zoom)
24 27 
 import(BiocParallel)
25 28 
 import(InteractionSet)
26 29 
 import(dplyr)
Browse code

version bump: 0.9.0

js2264 authored on 06/07/2022 20:04:56
Showing 1 changed files
NAMESPACE
History View file @ 789b6f6
... ... 
@@ -1,13 +1,11 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(APA)
4 
-export(addLoops)
5 
-export(addTads)
6 
-export(addTracks)
7 4 
 export(cool2gi)
8 5 
 export(cool2seqinfo)
9 6 
 export(detrend)
10 7 
 export(fetchCool)
8 
+export(formatCoords)
11 9 
 export(getAnchors)
12 10 
 export(getCounts)
13 11 
 export(getHicStats)
... ... 
@@ -22,16 +20,12 @@ export(lsCoolResolutions)
22 20 
 export(pairs2gi)
23 21 
 export(peekCool)
24 22 
 export(plotMatrix)
25 
-export(plotTriangularMatrix)
26 23 
 export(splitCoords)
27 24 
 import(BiocParallel)
28 25 
 import(InteractionSet)
29 
-import(corrr)
30 26 
 import(dplyr)
31 
-import(egg)
32 27 
 import(ggplot2)
33 28 
 import(ggrastr)
34 
-import(reticulate)
35 29 
 import(rhdf5)
36 30 
 import(scales)
37 31 
 import(stringr)
... ... 
@@ -50,11 +44,7 @@ importFrom(GenomicRanges,seqnames)
50 44 
 importFrom(GenomicRanges,start)
51 45 
 importFrom(GenomicRanges,width)
52 46 
 importFrom(IRanges,IRanges)
53 
-importFrom(IRanges,`%over%`)
54 
-importFrom(IRanges,subsetByOverlaps)
55 47 
 importFrom(S4Vectors,subjectHits)
56 
-importFrom(SummarizedExperiment,assay)
57 48 
 importFrom(glue,glue)
58 
-importFrom(purrr,map_dfr)
59 49 
 importFrom(scales,rescale)
60 50 
 importFrom(tibble,tibble)
Browse code

improve contacts

js2264 authored on 02/07/2022 11:47:22
Showing 1 changed files
NAMESPACE
History View file @ 84678e4
... ... 
@@ -6,7 +6,6 @@ export(addTads)
6 6 
 export(addTracks)
7 7 
 export(cool2gi)
8 8 
 export(cool2seqinfo)
9 
-export(correlateMatrix)
10 9 
 export(detrend)
11 10 
 export(fetchCool)
12 11 
 export(getAnchors)
... ... 
@@ -18,7 +17,6 @@ export(ggPs)
18 17 
 export(ggtheme_HiContacts)
19 18 
 export(ggtheme_HiContacts_tracks)
20 19 
 export(gi2cm)
21 
-export(iceGis)
22 20 
 export(lsCoolFiles)
23 21 
 export(lsCoolResolutions)
24 22 
 export(pairs2gi)
Browse code

feat: contacts class

js2264 authored on 29/06/2022 13:25:26
Showing 1 changed files
NAMESPACE
History View file @ 814522a
... ... 
@@ -1,32 +1,29 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(APA)
3 4 
 export(addLoops)
4 5 
 export(addTads)
5 6 
 export(addTracks)
6 7 
 export(cool2gi)
7 8 
 export(cool2seqinfo)
8 9 
 export(correlateMatrix)
10 
+export(detrend)
9 11 
 export(fetchCool)
10 12 
 export(getAnchors)
11 13 
 export(getCounts)
12 14 
 export(getHicStats)
13 15 
 export(getPs)
14 
-export(ggcorrmatrix)
15 
-export(ggmatrix)
16 
-export(ggtheme_coolerr)
17 
-export(ggtheme_coolerr_tracks)
18 
-export(ggtiltedmatrix)
16 
+export(ggMatrix)
17 
+export(ggPs)
18 
+export(ggtheme_HiContacts)
19 
+export(ggtheme_HiContacts_tracks)
19 20 
 export(gi2cm)
20 21 
 export(iceGis)
21 22 
 export(lsCoolFiles)
22 23 
 export(lsCoolResolutions)
23 
-export(normalizeOverExpected)
24 
+export(pairs2gi)
24 25 
 export(peekCool)
25 
-export(plotAggregatedMatrix)
26 
-export(plotCorrelatedMatrix)
27 26 
 export(plotMatrix)
28 
-export(plotMatrixList)
29 
-export(plotOverExpected)
30 27 
 export(plotTriangularMatrix)
31 28 
 export(splitCoords)
32 29 
 import(BiocParallel)
... ... 
@@ -59,8 +56,6 @@ importFrom(IRanges,`%over%`)
59 56 
 importFrom(IRanges,subsetByOverlaps)
60 57 
 importFrom(S4Vectors,subjectHits)
61 58 
 importFrom(SummarizedExperiment,assay)
62 
-importFrom(cowplot,get_legend)
63 
-importFrom(cowplot,plot_grid)
64 59 
 importFrom(glue,glue)
65 60 
 importFrom(purrr,map_dfr)
66 61 
 importFrom(scales,rescale)
Browse code

feat: plot ratio of maps with serpentine

js2264 authored on 23/06/2022 18:15:01
Showing 1 changed files
NAMESPACE
History View file @ 273cc73
... ... 
@@ -49,6 +49,7 @@ importFrom(GenomeInfoDb,seqlengths)
49 49 
 importFrom(GenomicRanges,GRanges)
50 50 
 importFrom(GenomicRanges,end)
51 51 
 importFrom(GenomicRanges,findOverlaps)
52 
+importFrom(GenomicRanges,mcols)
52 53 
 importFrom(GenomicRanges,resize)
53 54 
 importFrom(GenomicRanges,seqnames)
54 55 
 importFrom(GenomicRanges,start)
Browse code

doc

js2264 authored on 03/08/2021 15:56:56
Showing 1 changed files
NAMESPACE
History View file @ 079f18f
... ... 
@@ -1,5 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(addLoops)
4 
+export(addTads)
3 5 
 export(addTracks)
4 6 
 export(cool2gi)
5 7 
 export(cool2seqinfo)
... ... 
@@ -53,10 +55,12 @@ importFrom(GenomicRanges,start)
53 55 
 importFrom(GenomicRanges,width)
54 56 
 importFrom(IRanges,IRanges)
55 57 
 importFrom(IRanges,`%over%`)
58 
+importFrom(IRanges,subsetByOverlaps)
56 59 
 importFrom(S4Vectors,subjectHits)
57 60 
 importFrom(SummarizedExperiment,assay)
58 61 
 importFrom(cowplot,get_legend)
59 62 
 importFrom(cowplot,plot_grid)
60 63 
 importFrom(glue,glue)
64 
+importFrom(purrr,map_dfr)
61 65 
 importFrom(scales,rescale)
62 66 
 importFrom(tibble,tibble)
Browse code

fix: matrix over expected

js2264 authored on 28/07/2021 13:17:20
Showing 1 changed files
NAMESPACE
History View file @ e3fbb54
... ... 
@@ -15,12 +15,10 @@ export(ggtheme_coolerr)
15 15 
 export(ggtheme_coolerr_tracks)
16 16 
 export(ggtiltedmatrix)
17 17 
 export(gi2cm)
18 
-export(gi2mat)
19 18 
 export(iceGis)
20 19 
 export(lsCoolFiles)
21 20 
 export(lsCoolResolutions)
22 21 
 export(normalizeOverExpected)
23 
-export(pairs2gi)
24 22 
 export(peekCool)
25 23 
 export(plotAggregatedMatrix)
26 24 
 export(plotCorrelatedMatrix)
... ... 
@@ -59,7 +57,6 @@ importFrom(S4Vectors,subjectHits)
59 57 
 importFrom(SummarizedExperiment,assay)
60 58 
 importFrom(cowplot,get_legend)
61 59 
 importFrom(cowplot,plot_grid)
62 
-importFrom(dplyr,mutate)
63 60 
 importFrom(glue,glue)
64 
-importFrom(purrr,set_names)
65 
-importFrom(vroom,vroom)
61 
+importFrom(scales,rescale)
62 
+importFrom(tibble,tibble)
Browse code

fix: triangular matrices

js2264 authored on 28/07/2021 11:16:23
Showing 1 changed files
NAMESPACE
History View file @ ced087e
... ... 
@@ -57,6 +57,8 @@ importFrom(IRanges,IRanges)
57 57 
 importFrom(IRanges,`%over%`)
58 58 
 importFrom(S4Vectors,subjectHits)
59 59 
 importFrom(SummarizedExperiment,assay)
60 
+importFrom(cowplot,get_legend)
61 
+importFrom(cowplot,plot_grid)
60 62 
 importFrom(dplyr,mutate)
61 63 
 importFrom(glue,glue)
62 64 
 importFrom(purrr,set_names)
Browse code

fix: imports

js2264 authored on 23/07/2021 16:59:30
Showing 1 changed files
NAMESPACE
History View file @ 4ea925d
... ... 
@@ -30,7 +30,6 @@ export(plotOverExpected)
30 30 
 export(plotTriangularMatrix)
31 31 
 export(splitCoords)
32 32 
 import(BiocParallel)
33 
-import(GenomicRanges)
34 33 
 import(InteractionSet)
35 34 
 import(corrr)
36 35 
 import(dplyr)
Browse code

feat: read pairs file and hicstuff log

js2264 authored on 23/07/2021 15:15:24
Showing 1 changed files
NAMESPACE
History View file @ 3dd79e7
... ... 
@@ -7,6 +7,8 @@ export(correlateMatrix)
7 7 
 export(fetchCool)
8 8 
 export(getAnchors)
9 9 
 export(getCounts)
10 
+export(getHicStats)
11 
+export(getPs)
10 12 
 export(ggcorrmatrix)
11 13 
 export(ggmatrix)
12 14 
 export(ggtheme_coolerr)
... ... 
@@ -18,6 +20,7 @@ export(iceGis)
18 20 
 export(lsCoolFiles)
19 21 
 export(lsCoolResolutions)
20 22 
 export(normalizeOverExpected)
23 
+export(pairs2gi)
21 24 
 export(peekCool)
22 25 
 export(plotAggregatedMatrix)
23 26 
 export(plotCorrelatedMatrix)
... ... 
@@ -27,6 +30,7 @@ export(plotOverExpected)
27 30 
 export(plotTriangularMatrix)
28 31 
 export(splitCoords)
29 32 
 import(BiocParallel)
33 
+import(GenomicRanges)
30 34 
 import(InteractionSet)
31 35 
 import(corrr)
32 36 
 import(dplyr)
... ... 
@@ -54,4 +58,7 @@ importFrom(IRanges,IRanges)
54 58 
 importFrom(IRanges,`%over%`)
55 59 
 importFrom(S4Vectors,subjectHits)
56 60 
 importFrom(SummarizedExperiment,assay)
61 
+importFrom(dplyr,mutate)
57 62 
 importFrom(glue,glue)
63 
+importFrom(purrr,set_names)
64 
+importFrom(vroom,vroom)
Browse code

feat: plotting autocorrelation matrix

js2264 authored on 15/07/2021 18:40:50
Showing 1 changed files
NAMESPACE
History View file @ 5fa20a9
... ... 
@@ -3,9 +3,11 @@
3 3 
 export(addTracks)
4 4 
 export(cool2gi)
5 5 
 export(cool2seqinfo)
6 
+export(correlateMatrix)
6 7 
 export(fetchCool)
7 8 
 export(getAnchors)
8 9 
 export(getCounts)
10 
+export(ggcorrmatrix)
9 11 
 export(ggmatrix)
10 12 
 export(ggtheme_coolerr)
11 13 
 export(ggtheme_coolerr_tracks)
... ... 
@@ -18,6 +20,7 @@ export(lsCoolResolutions)
18 20 
 export(normalizeOverExpected)
19 21 
 export(peekCool)
20 22 
 export(plotAggregatedMatrix)
23 
+export(plotCorrelatedMatrix)
21 24 
 export(plotMatrix)
22 25 
 export(plotMatrixList)
23 26 
 export(plotOverExpected)
... ... 
@@ -25,6 +28,7 @@ export(plotTriangularMatrix)
25 28 
 export(splitCoords)
26 29 
 import(BiocParallel)
27 30 
 import(InteractionSet)
31 
+import(corrr)
28 32 
 import(dplyr)
29 33 
 import(egg)
30 34 
 import(ggplot2)
Browse code

docs: improve function doc

js2264 authored on 13/07/2021 11:11:01
Showing 1 changed files
NAMESPACE
History View file @ 78cbc41
... ... 
@@ -24,18 +24,11 @@ export(plotOverExpected)
24 24 
 export(plotTriangularMatrix)
25 25 
 export(splitCoords)
26 26 
 import(BiocParallel)
27 
-import(GenomeInfoDb)
28 
-import(GenomicRanges)
29 
-import(IRanges)
30 27 
 import(InteractionSet)
31 
-import(S4Vectors)
32 
-import(SummarizedExperiment)
33 28 
 import(dplyr)
34 29 
 import(egg)
35 30 
 import(ggplot2)
36 31 
 import(ggrastr)
37 
-import(glue)
38 
-import(magrittr)
39 32 
 import(reticulate)
40 33 
 import(rhdf5)
41 34 
 import(scales)
... ... 
@@ -44,3 +37,17 @@ import(tibble)
44 37 
 import(tidyr)
45 38 
 import(tools)
46 39 
 import(zeallot)
40 
+importFrom(GenomeInfoDb,Seqinfo)
41 
+importFrom(GenomeInfoDb,seqlengths)
42 
+importFrom(GenomicRanges,GRanges)
43 
+importFrom(GenomicRanges,end)
44 
+importFrom(GenomicRanges,findOverlaps)
45 
+importFrom(GenomicRanges,resize)
46 
+importFrom(GenomicRanges,seqnames)
47 
+importFrom(GenomicRanges,start)
48 
+importFrom(GenomicRanges,width)
49 
+importFrom(IRanges,IRanges)
50 
+importFrom(IRanges,`%over%`)
51 
+importFrom(S4Vectors,subjectHits)
52 
+importFrom(SummarizedExperiment,assay)
53 
+importFrom(glue,glue)
Browse code

docs: add documentation

js2264 authored on 13/07/2021 09:22:38
Showing 1 changed files
NAMESPACE
History View file @ f46d139
... ... 
@@ -1,2 +1,46 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(addTracks)
4 
+export(cool2gi)
5 
+export(cool2seqinfo)
6 
+export(fetchCool)
7 
+export(getAnchors)
8 
+export(getCounts)
9 
+export(ggmatrix)
10 
+export(ggtheme_coolerr)
11 
+export(ggtheme_coolerr_tracks)
12 
+export(ggtiltedmatrix)
13 
+export(gi2cm)
14 
+export(gi2mat)
15 
+export(iceGis)
16 
+export(lsCoolFiles)
17 
+export(lsCoolResolutions)
18 
+export(normalizeOverExpected)
19 
+export(peekCool)
20 
+export(plotAggregatedMatrix)
21 
+export(plotMatrix)
22 
+export(plotMatrixList)
23 
+export(plotOverExpected)
24 
+export(plotTriangularMatrix)
25 
+export(splitCoords)
26 
+import(BiocParallel)
27 
+import(GenomeInfoDb)
28 
+import(GenomicRanges)
29 
+import(IRanges)
30 
+import(InteractionSet)
31 
+import(S4Vectors)
32 
+import(SummarizedExperiment)
33 
+import(dplyr)
34 
+import(egg)
35 
+import(ggplot2)
36 
+import(ggrastr)
37 
+import(glue)
38 
+import(magrittr)
39 
+import(reticulate)
40 
+import(rhdf5)
41 
+import(scales)
42 
+import(stringr)
43 
+import(tibble)
44 
+import(tidyr)
45 
+import(tools)
46 
+import(zeallot)
Browse code

Initial commit

js2264 authored on 16/06/2021 10:42:24
Showing 1 changed files
NAMESPACE
History View file @ 74f163e
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,2 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+