1. sevenC
  2. Commit 3b17dcb0f0764507b64e7998dd90da1adc6f17be
Browse code

change range to 30Mb on chr22 for example ChIP-seq data

ibn-salem authored on 30/03/2018 17:11:35
Showing 21 changed files
R/interaction.R
History View file @ 3b17dcb
... ... 
@@ -115,7 +115,7 @@ noZeroVar <- function(dat) {
115 115 
 #'
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 #'   # use example bigWig file
117 117 
 #'  exampleBigWig <- system.file("extdata",
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-#'      "GM12878_Stat1.chr22_1-18000000.bigWig", package = "sevenC")
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+#'      "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")
119 119 
 #'
120 120 
 #'   # add coverage from bigWig file
121 121 
 #'   motifGR <- addCovToGR(motifGR, exampleBigWig)
... ... 
@@ -532,7 +532,7 @@ prepareCisPairs <- function(motifs, maxDist = 1e6, scoreColname = "score"){
532 532 
 #'
533 533 
 #'  # use example bigWig file of ChIP-seq signals on human chromosome 22
534 534 
 #'  exampleBigWig <- system.file("extdata",
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-#'  "GM12878_Stat1.chr22_1-18000000.bigWig", package = "sevenC")
535 
+#'  "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")
536 536 
 #'
537 537 
 #'  # use example CTCF moitf location on human chromosome 22
538 538 
 #'  motifGR <- sevenC::motif.hg19.CTCF.chr22
R/parseChIP-seq.R
History View file @ 3b17dcb
... ... 
@@ -94,7 +94,7 @@ slideMean <- function(x, k){
94 94 
 #'
95 95 
 #'  # use example bigWig file of ChIP-seq signals on human chromosome 22
96 96 
 #'  exampleBigWig <- system.file("extdata",
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-#'  "GM12878_Stat1.chr22_1-18000000.bigWig", package = "sevenC")
97 
+#'  "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")
98 98 
 #'
99 99 
 #'  # use example CTCF moitf location on human chromosome 22
100 100 
 #'  motifGR <- sevenC::motif.hg19.CTCF.chr22
R/parseInteractions.R
History View file @ 3b17dcb
... ... 
@@ -11,7 +11,7 @@
11 11 
 #'
12 12 
 #' # use example loop file
13 13 
 #'exampleLoopFile <- system.file("extdata",
14 
-#'   "GM12878_HiCCUPS.chr22_1-18000000.loop.txt", package = "sevenC")
14 
+#'   "GM12878_HiCCUPS.chr22_1-30000000.loop.txt", package = "sevenC")
15 15 
 #'
16 16 
 #'# read loops form example file:
17 17 
 #'gi <- parseLoopsRao(exampleLoopFile)
... ... 
@@ -86,7 +86,7 @@ parseLoopsRao <- function(inFile, ...){
86 86 
 #'
87 87 
 #' @examples
88 88 
 #'exampleLoopTang2015File <- system.file("extdata",
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-#'    "ChIA-PET_GM12878_Tang2015.chr22_1-18000000.clusters.txt",
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+#'    "ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt",
90 90 
 #'    package = "sevenC")
91 91 
 #'
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 #'gi <- parseLoopsTang2015(exampleLoopTang2015File)
README.md
History View file @ 3b17dcb
... ... 
@@ -62,7 +62,7 @@ gi <- prepareCisPairs(motifs, maxDist = 10^6)
62 62
63 63 
 ```R
64 64 
 # use example ChIP-seq bigWig file
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-bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
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+bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
66 66 
   package = "sevenC")
67 67
68 68 
 # add ChIP-seq coverage and compute correaltion at motif pairs
data-raw/download-raw-data.R
History View file @ 3b17dcb
... ... 
@@ -7,7 +7,7 @@ require(tidyverse)
7 7
8 8 
 bwURLstr <- "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat1StdSig.bigWig"
9 9 
 bwTmpFile <- "data-raw/GM12878_Stat1.bigWig"
10 
-bwFinalFile <- "inst/extdata/GM12878_Stat1.chr22_1-18000000.bigWig"
10 
+bwFinalFile <- "inst/extdata/GM12878_Stat1.chr22_1-30000000.bigWig"
11 11 
 dir.create("inst/extdata", recursive = TRUE)
12 12
13 13 
 #require(RCurl)
... ... 
@@ -15,15 +15,19 @@ dir.create("inst/extdata", recursive = TRUE)
15 15
16 16 
 download.file(bwURLstr, destfile = bwTmpFile)
17 17
18 
+# read bigWig file as GRanges
18 19 
 bw <- rtracklayer::import(bwTmpFile)
20 
+
21 
+# get subset on chr22 1:30000000
19 22 
 bwSub <- IRanges::subsetByOverlaps(
20 
-  bw, GenomicRanges::GRanges("chr22", IRanges::IRanges(1, 18000000))
21 
-  )
23 
+  bw, GenomicRanges::GRanges("chr22", IRanges::IRanges(1, 30000000))
24 
+)
22 25
23 
-print(object.size(bwSub), unit = "Kb")
26 
+print(object.size(bwSub), unit = "Mb")
24 27
25 28 
 # save subset of file in inst/extdata as bigWig file
26 29 
 rtracklayer::export(bwSub, con = bwFinalFile, format = "bigWig")
30 
+# rtracklayer::export(bwChr22, con = bwFinalFile, format = "bigWig")
27 31
28 32 
 #*******************************************************************************
29 33 
 # add CTCF moitif locations in human genome from JASPAR motif tracks      ------
... ... 
@@ -133,19 +137,19 @@ tmp <- tempfile()
133 137
134 138 
 download.file(loopURL, tmp)
135 139
136 
-df <- read.table(gzfile(tmp), header=TRUE)
140 
+df <- read.table(gzfile(tmp), header = TRUE)
137 141
138 142 
 # filter for only chromosome 22 in some start region
139 143 
 fltDF <- subset(df, chr1 == 22 &
140 144 
                   chr2 == 22 &
141 
-                  x2 <= 18000000 &
142 
-                  y2 <= 18000000)
145 
+                  x2 <= 30000000 &
146 
+                  y2 <= 30000000)
143 147
144 148 
 # save subset of file in inst/extdata as raw .txt file
145 
-loopFinalFile <- "inst/extdata/GM12878_HiCCUPS.chr22_1-18000000.loop.txt"
149 
+loopFinalFile <- "inst/extdata/GM12878_HiCCUPS.chr22_1-30000000.loop.txt"
146 150
147 
-write.table(fltDF, file=loopFinalFile, col.names = TRUE, row.names=FALSE,
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-            quote=FALSE, sep="\t")
151 
+write.table(fltDF, file = loopFinalFile, col.names = TRUE, row.names = FALSE,
152 
+            quote = FALSE, sep = "\t")
149 153
150 154 
 #-------------------------------------------------------------------------------
151 155 
 # Download sample ChIA-pet data from Tang et al. 2015 Cell
... ... 
@@ -160,13 +164,13 @@ df <- read.table(gzfile(tmp), header = FALSE)
160 164 
 # filter for only chromosome 22 in some start region
161 165 
 fltDF <- subset(df, V1 == "chr22" &
162 166 
                   V4 == "chr22" &
163 
-                  V3 <= 18000000 &
164 
-                  V6 <= 18000000)
167 
+                  V3 <= 30000000 &
168 
+                  V6 <= 30000000)
165 169
166 170 
 # save subset of file in inst/extdata as raw .txt file
167 
-loopFinalFile <- "inst/extdata/ChIA-PET_GM12878_Tang2015.chr22_1-18000000.clusters.txt"
171 
+loopFinalFile <- "inst/extdata/ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt"
168 172
169 
-write.table(fltDF, file=loopFinalFile, col.names = FALSE, row.names = FALSE,
173 
+write.table(fltDF, file = loopFinalFile, col.names = FALSE, row.names = FALSE,
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             quote = FALSE, sep = "\t")
171 175
172 176
data/motif.hg19.CTCF.chr22.cov.rda
History View file @ 3b17dcb
173 177 
Binary files a/data/motif.hg19.CTCF.chr22.cov.rda and b/data/motif.hg19.CTCF.chr22.cov.rda differ
inst/extdata/ChIA-PET_GM12878_Tang2015.chr22_1-18000000.clusters.txt
History View file @ 3b17dcb
174 178 
deleted file mode 100644
... ... 
@@ -1,26 +0,0 @@
1 
-chr22	17651958	17652963	chr22	17738917	17739494	6
2 
-chr22	17564978	17566375	chr22	17652325	17653688	6
3 
-chr22	17652354	17653076	chr22	17748981	17750426	10
4 
-chr22	17397509	17398723	chr22	17979868	17981155	17
5 
-chr22	17640752	17641588	chr22	17980101	17981341	4
6 
-chr22	17695013	17696898	chr22	17980786	17981127	5
7 
-chr22	17397232	17400263	chr22	17537636	17539682	69
8 
-chr22	17601224	17601467	chr22	17980285	17981084	4
9 
-chr22	17555388	17557478	chr22	17651113	17653869	64
10 
-chr22	17554865	17558708	chr22	17979333	17981442	56
11 
-chr22	17397921	17399013	chr22	17541337	17541796	4
12 
-chr22	17640126	17640850	chr22	17651859	17653023	7
13 
-chr22	17847376	17848310	chr22	17980722	17980935	4
14 
-chr22	17648674	17650395	chr22	17979831	17981161	11
15 
-chr22	17398399	17398792	chr22	17490475	17491031	4
16 
-chr22	17558155	17558799	chr22	17652163	17653052	4
17 
-chr22	17749075	17749931	chr22	17980027	17981197	12
18 
-chr22	17413070	17414059	chr22	17652398	17652941	6
19 
-chr22	17413217	17413877	chr22	17538572	17539505	10
20 
-chr22	17398073	17399492	chr22	17651916	17653377	12
21 
-chr22	17398001	17398547	chr22	17977913	17978705	4
22 
-chr22	17555600	17556240	chr22	17587550	17587925	4
23 
-chr22	17651241	17653832	chr22	17977418	17982442	219
24 
-chr22	17693303	17694414	chr22	17980499	17981503	5
25 
-chr22	17686000	17687085	chr22	17980014	17981343	33
26 
-chr22	17397960	17399634	chr22	17534857	17537064	14
inst/extdata/ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt
History View file @ 3b17dcb
27 0 
new file mode 100644
... ... 
@@ -0,0 +1,675 @@
1 
+chr22	23034491	23036670	chr22	23283912	23285694	35
2 
+chr22	17651958	17652963	chr22	17738917	17739494	6
3 
+chr22	25597967	25598936	chr22	26173795	26174818	13
4 
+chr22	22510616	22512455	chr22	22521468	22523077	16
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+chr22	22509532	22514342	chr22	22548552	22551160	87
6 
+chr22	18941876	18942809	chr22	19464943	19465584	4
7 
+chr22	19287031	19287973	chr22	19464562	19465851	13
8 
+chr22	18312803	18313722	chr22	18373765	18375006	7
9 
+chr22	17564978	17566375	chr22	17652325	17653688	6
10 
+chr22	25476828	25477694	chr22	25729164	25730588	12
11 
+chr22	23516188	23516670	chr22	23881715	23882050	4
12 
+chr22	19132082	19132502	chr22	19461126	19462184	8
13 
+chr22	26173898	26174558	chr22	26726668	26727254	7
14 
+chr22	22067582	22067952	chr22	23296966	23297387	4
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+chr22	26292017	26293264	chr22	26725776	26727375	21
16 
+chr22	26249784	26250802	chr22	26726543	26727277	12
17 
+chr22	22307042	22307729	chr22	23298044	23298722	6
18 
+chr22	25198954	25199580	chr22	25246180	25247528	9
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inst/extdata/GM12878_HiCCUPS.chr22_1-18000000.loop.txt
History View file @ 3b17dcb
0 676 
deleted file mode 100644
... ... 
@@ -1,4 +0,0 @@
1 
-chr1	x1	x2	chr2	y1	y2	color	o	e_bl	e_donut	e_h	e_v	fdr_bl	fdr_donut	fdr_h	fdr_v	num_collapsed	centroid1	centroid2	radius	motif_x1	motif_x2	sequence_1	orientation_1	uniqueness_1	motif_y1	motif_y2	sequence2	orientation_2	uniqueness_2
2 
-22	17395000	17400000	22	17535000	17540000	0,255,255	197	67.4175	55.7138	57.5168	67.4858	7.47260877489e-25	9.06654965496e-37	1.919084112e-36	1.37131649771e-24	9	17400277	17540277	12533.9046363	17398481	17398501	ATGGCCACAGGGGGGCAGTC	p	u	17539262	17539282	ATTGCCAGGAGAGGGCAGCA	n	u
3 
-22	17400000	17410000	22	17980000	17990000	0,255,255	93	47.0087	39.5654	42.1916	43.4847	2.62232767072e-05	3.13709922573e-05	4.47275961564e-05	4.57189135069e-05	3	17398333	17981666	7453.559925	17398481	17398501	ATGGCCACAGGGGGGCAGTC	p	u	17980898	17980918	GTCACCAGTAGAGGGTAGCA	n	u
4 
-22	17650000	17655000	22	17980000	17985000	0,255,255	128	52.6055	47.3593	51.9744	62.5858	4.71722890801e-10	1.20308682759e-16	7.25734272823e-10	7.99193200106e-05	5	17654500	17981500	6324.55532034	17652499	17652519	GCGGCCGGCAGGGGGCAGCA	p	i	17980898	17980918	GTCACCAGTAGAGGGTAGCA	n	u
inst/extdata/GM12878_HiCCUPS.chr22_1-30000000.loop.txt
History View file @ 3b17dcb
5 0 
new file mode 100644
... ... 
@@ -0,0 +1,60 @@
1 
+chr1	x1	x2	chr2	y1	y2	color	o	e_bl	e_donut	e_h	e_v	fdr_bl	fdr_donut	fdr_h	fdr_v	num_collapsed	centroid1	centroid2	radius	motif_x1	motif_x2	sequence_1	orientation_1	uniqueness_1	motif_y1	motif_y2	sequence2	orientation_2	uniqueness_2
2 
+22	17395000	17400000	22	17535000	17540000	0,255,255	197	67.4175	55.7138	57.5168	67.4858	7.47260877489e-25	9.06654965496e-37	1.919084112e-36	1.37131649771e-24	9	17400277	17540277	12533.9046363	17398481	17398501	ATGGCCACAGGGGGGCAGTC	p	u	17539262	17539282	ATTGCCAGGAGAGGGCAGCA	n	u
3 
+22	17400000	17410000	22	17980000	17990000	0,255,255	93	47.0087	39.5654	42.1916	43.4847	2.62232767072e-05	3.13709922573e-05	4.47275961564e-05	4.57189135069e-05	3	17398333	17981666	7453.559925	17398481	17398501	ATGGCCACAGGGGGGCAGTC	p	u	17980898	17980918	GTCACCAGTAGAGGGTAGCA	n	u
4 
+22	17650000	17655000	22	17980000	17985000	0,255,255	128	52.6055	47.3593	51.9744	62.5858	4.71722890801e-10	1.20308682759e-16	7.25734272823e-10	7.99193200106e-05	5	17654500	17981500	6324.55532034	17652499	17652519	GCGGCCGGCAGGGGGCAGCA	p	i	17980898	17980918	GTCACCAGTAGAGGGTAGCA	n	u
5 
+22	17690000	17700000	22	18250000	18260000	0,255,255	97	44.8518	46.3288	47.2751	52.1945	2.58023249606e-06	3.04342737504e-06	4.49423661001e-06	0.0113682385563	2	17700000	18255000	5000	17695055	17695075	GCCCCCAGTAGGGAGCAGCA	p	i	NA	NA	NA	NA	NA
6 
+22	18310000	18315000	22	18550000	18555000	0,255,255	276	116.321	116.952	135.96	149.765	2.18724420189e-27	2.73199271911e-27	1.72921637579e-14	1.67946323355e-14	7	18313214	18555357	7889.5435837	18312919	18312939	TTCTACAGCAGGGGGAGCCA	p	u	18558983	18559003	TTGTCCAGGAGATGGAGGCA	n	i
7 
+22	18590000	18595000	22	18625000	18630000	0,255,255	153	70.5085	85.7398	80.6793	85.1993	1.06315382013e-10	6.22113685834e-05	8.81418439583e-05	8.55860331032e-05	2	18592500	18630000	2500	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
8 
+22	18940000	18950000	22	20260000	20270000	0,255,255	41	3.46394	4.31532	3.78421	3.21359	8.68630691167e-23	1.9853018122e-18	6.44737420602e-22	9.79694047326e-22	2	18950000	20260000	7071.06781187	18942095	18942115	GCGGCCGGCGGAGGGCAGCA	p	u	20273423	20273443	GCGGCCGGCAGAGGGCAGCA	n	u
9 
+22	19160000	19165000	22	19460000	19465000	0,255,255	69	25.1988	27.8883	34.0333	29.4023	7.86012853579e-06	7.43683295365e-06	0.00581804303897	1.28105959517e-05	1	19162500	19462500	0	19167091	19167111	CTGGCCTGGAGGGGGCAGCT	p	u	NA	NA	NA	NA	NA
10 
+22	19720000	19725000	22	19900000	19905000	0,255,255	178	77.9374	74.9071	95.8726	90.6867	4.87614551392e-10	3.30852729321e-18	8.87709311594e-10	8.66515395622e-10	12	19720416	19897916	13705.7368362	19718333	19718353	GCAGGCACCAGAGGGCGCTC	p	u	19897632	19897652	GAGACCACCAGAGGGCGGCA	n	u
11 
+22	20145000	20150000	22	20270000	20275000	0,255,255	94	36.0823	35.7978	44.527	36.6134	5.24301962982e-10	4.31848838933e-10	1.44644670898e-05	8.91867839469e-10	6	20142500	20266666	14166.6666667	20144689	20144709	CTCACCACCAGATGGCACCA	p	u	20273423	20273443	GCGGCCGGCAGAGGGCAGCA	n	u
12 
+22	20765000	20770000	22	20810000	20815000	0,255,255	225	104.192	115.178	124.193	127.021	4.98909643168e-13	6.9834080639e-13	3.99248754501e-05	3.96572961866e-05	6	20772500	20811666	7682.95371441	20772592	20772612	CCAGCCGCCAGATGGCAGCA	p	u	20810711	20810731	TTGGCCACAGAGGGGCAGCC	n	u
13 
+22	20770000	20780000	22	21050000	21060000	0,255,255	68	27.8868	28.1258	31.9776	30.1549	1.85761393954e-05	2.54702234636e-05	0.0153965760843	3.14082560521e-05	1	20775000	21055000	0	20772592	20772612	CCAGCCGCCAGATGGCAGCA	p	u	21052004	21052024	GCAGCCACCTGAGGGCGCCC	n	u
14 
+22	20940000	20950000	22	21050000	21060000	0,255,255	208	92.5982	92.8678	103.688	117.297	9.15825480107e-18	7.54081567298e-18	9.35304505484e-09	9.3938958791e-09	3	20941666	21051666	7453.559925	NA	NA	NA	NA	NA	21052004	21052024	GCAGCCACCTGAGGGCGCCC	n	u
15 
+22	20960000	20965000	22	21040000	21045000	0,255,255	121	44.2344	49.9662	52.4789	63.7325	6.19839591221e-14	3.69141607237e-08	5.8757243904e-08	0.00129605308507	4	20960000	21048750	6731.45600892	20960663	20960683	ACGTCCCCCAGAGGGCGCAG	p	u	NA	NA	NA	NA	NA
16 
+22	22060000	22065000	22	22295000	22300000	0,255,255	130	68.8559	64.092	72.2118	79.3357	1.8120961992e-05	2.30708514522e-05	3.41565045368e-05	0.0878544236604	7	22065357	22298928	8835.22634061	22067627	22067647	ACAGCCACGAGGGGGAAGCA	p	u	22293084	22293104	GGTGCCACAAGGGGGTAGCA	n	i
17 
+22	22380000	22385000	22	23250000	23255000	0,255,255	51	7.23807	16.1029	22.3623	23.245	8.18035021993e-20	1.54355883859e-05	0.00402210845168	0.00410067890286	1	22382500	23252500	0	22385047	22385067	CTAGGCAGAAGGGGGTGCTG	p	u	NA	NA	NA	NA	NA
18 
+22	22380000	22390000	22	23280000	23290000	0,255,255	223	81.9943	97.6436	95.3845	128.276	1.58440520929e-22	3.25757701835e-12	2.69414172985e-22	0.000137028416217	5	22393000	23287000	23409.3998214	22385047	22385067	CTAGGCAGAAGGGGGTGCTG	p	u	NA	NA	NA	NA	NA
19 
+22	22520000	22525000	22	23480000	23485000	0,255,255	33	14.6214	14.3818	15.4993	15.4353	0.0703123828241	0.0900519464466	0.0980803257417	0.0999694312093	2	22522500	23480000	2500	22526156	22526176	ATCACCAGCAGGAGGATCCT	p	i	NA	NA	NA	NA	NA
20 
+22	22535000	22540000	22	23245000	23250000	0,255,255	61	3.58412	16.5599	23.9156	19.3572	5.32296488574e-44	1.3819169839e-09	4.32359319842e-06	1.95327507128e-09	4	22546250	23250000	9762.81209488	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
21 
+22	22535000	22540000	22	23285000	23290000	0,255,255	99	25.3034	34.4312	52.8765	36.6322	1.82312125421e-17	6.99580030345e-12	0.00312921841303	1.5520656924e-11	12	22537916	23290000	17144.2005095	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
22 
+22	22705000	22710000	22	23280000	23285000	0,255,255	41	8.68894	11.6968	17.5072	10.4691	2.1946541907e-09	2.08695409485e-06	0.0244307798169	2.10189679984e-06	3	22705833	23287500	6009.25212577	22711805	22711825	CTGGACACTAGGGGGCGCTT	p	u	NA	NA	NA	NA	NA
23 
+22	22930000	22940000	22	23030000	23040000	0,255,255	394	193.095	187.944	214.402	227.649	3.98746115105e-14	3.39196769278e-30	6.80164568449e-14	6.84914449438e-14	4	22937500	23035000	10307.764064	NA	NA	NA	NA	NA	23030277	23030297	GTGCCCAATAGATGGTGCTG	n	i
24 
+22	23155000	23160000	22	23190000	23195000	0,255,255	244	109.173	137.894	136.511	141.262	7.85680796242e-18	3.12276232994e-08	4.44109157456e-08	4.47736951388e-08	7	23151785	23192500	9285.71428571	23152640	23152660	TCCACCAGCAAGGGGCAGCA	p	i	NA	NA	NA	NA	NA
25 
+22	23170000	23180000	22	23630000	23640000	0,255,255	91	35.2192	42.2174	44.1384	48.0148	6.13397750344e-09	9.44778914514e-05	0.000132666904549	0.000135970820429	1	23175000	23635000	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
26 
+22	23195000	23200000	22	23280000	23285000	0,255,255	322	71.0397	85.2861	109.119	134.119	7.34805032936e-86	6.4199508556e-64	1.47229276061e-43	1.66597317696e-26	20	23201750	23283750	49392.5601685	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
27 
+22	23300000	23305000	22	23625000	23630000	0,255,255	60	23.448	20.0055	24.3541	22.3227	5.62831242797e-06	5.71240337925e-06	9.31792207248e-06	9.49321709768e-06	2	23302500	23625000	2500	23301569	23301589	TTGCCCACCAGGTGGCGGAA	p	i	NA	NA	NA	NA	NA
28 
+22	23300000	23310000	22	23720000	23730000	0,255,255	106	58.6868	44.9122	52.1668	48.8252	0.000180393174629	8.42000157796e-09	0.000283942592566	1.39837173918e-08	1	23305000	23725000	0	23301569	23301589	TTGCCCACCAGGTGGCGGAA	p	i	NA	NA	NA	NA	NA
29 
+22	23305000	23310000	22	23465000	23470000	0,255,255	272	89.3506	67.9156	94.0195	75.4582	3.95565294758e-41	1.09993327925e-58	8.55834592052e-41	4.32660480624e-58	15	23306833	23468500	12238.3731671	23301569	23301589	TTGCCCACCAGGTGGCGGAA	p	i	23470787	23470807	GTAACCAGGAGGGGGCACCC	n	u
30 
+22	23520000	23525000	22	23620000	23625000	0,255,255	300	98.7174	99.2284	115.489	124.116	1.30522103017e-35	1.53832359874e-35	3.00044646278e-35	2.26640666631e-20	23	23520760	23623804	15857.6488912	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
31 
+22	23680000	23690000	22	25070000	25080000	0,255,255	26	0.780614	1.10962	1.96323	1.76198	2.23731029651e-19	6.2649492803e-19	4.79984084272e-15	1.11005407079e-14	3	23688333	25071666	7453.559925	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
32 
+22	23880000	23890000	22	24100000	24110000	0,255,255	118	63.9117	54.3168	68.1508	53.7371	0.00427860793448	3.90951178838e-07	0.006284454227	5.93290913382e-07	1	23885000	24105000	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
33 
+22	23885000	23890000	22	24190000	24195000	0,255,255	62	16.0271	18.2757	20.6578	21.7489	4.57909557669e-10	4.87578433763e-10	1.95363637091e-06	1.94923613728e-06	3	23885833	24190833	3726.7799625	NA	NA	NA	NA	NA	24191889	24191909	CCGGCCGCGAGGGGGCGACA	n	i
34 
+22	23935000	23940000	22	25830000	25835000	0,255,255	17	0.572185	0.556796	0.590323	1.06821	5.60867512099e-08	2.86020468732e-07	1.80851106222e-07	3.61513166239e-07	1	23937500	25832500	0	23933472	23933492	GAGGCCACCAGGGGGTGCTG	n	u	NA	NA	NA	NA	NA
35 
+22	23970000	23980000	22	24190000	24200000	0,255,255	140	60.1181	65.0827	61.8489	89.3842	1.59379287698e-13	3.19781853125e-07	4.79134958965e-07	0.0117241034488	1	23975000	24195000	0	NA	NA	NA	NA	NA	24191889	24191909	CCGGCCGCGAGGGGGCGACA	n	i
36 
+22	23980000	23985000	22	25710000	25715000	0,255,255	35	0.448431	0.443458	0.480947	0.652763	3.98471758704e-31	4.49702764999e-30	2.0844697284e-30	4.01201075444e-30	1	23982500	25712500	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
37 
+22	24110000	24115000	22	24190000	24195000	0,255,255	214	81.1712	72.6876	78.2681	89.4125	6.99499314238e-20	1.11300020031e-31	1.25864734072e-19	1.24746168923e-19	7	24108928	24186785	12777.5313	NA	NA	NA	NA	NA	24191889	24191909	CCGGCCGCGAGGGGGCGACA	n	i
38 
+22	24715000	24720000	22	24915000	24920000	0,255,255	158	77.6638	78.5629	92.4564	92.1661	5.99091388035e-06	8.40996981128e-06	1.19714055356e-05	1.16317873835e-05	8	24721875	24921250	11267.3477358	24721175	24721195	GAAGACAGTAGATGGCAGTG	p	u	NA	NA	NA	NA	NA
39 
+22	24820000	24830000	22	24910000	24920000	0,255,255	1038	448.863	465.7	547.586	518.475	2.02839070116e-90	2.2576272255e-90	1.62273448757e-44	1.9337869087e-44	11	24819545	24911363	22508.0334603	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
40 
+22	25030000	25040000	22	25140000	25150000	0,255,255	84	39.9248	40.4949	43.9382	48.2354	0.00230878725921	0.00298957187341	0.00386341091471	0.00398598533913	1	25035000	25145000	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
41 
+22	25690000	25695000	22	25985000	25990000	0,255,255	55	2.98858	3.66937	5.25275	4.72503	3.01471912976e-42	6.55420066788e-37	1.07694791307e-26	1.88057751223e-31	3	25690833	25990833	13437.0962472	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
42 
+22	25850000	25860000	22	26720000	26730000	0,255,255	76	29.3392	29.4228	32.4632	31.7335	4.38157789307e-08	6.36181304194e-08	0.000267940599892	0.000269312981544	3	25861666	26728333	7453.559925	25858674	25858694	GCAGCCACCAGGTGTCAGCA	p	u	26727149	26727169	CTCACCTGCAGAGGGCAGTG	n	u
43 
+22	25855000	25860000	22	26170000	26175000	0,255,255	126	52.0183	43.3613	59.6222	46.362	1.73209331951e-09	6.94037484699e-16	2.66669380958e-09	1.57847825202e-15	8	25858125	26168125	11490.4851943	25858674	25858694	GCAGCCACCAGGTGTCAGCA	p	u	NA	NA	NA	NA	NA
44 
+22	26170000	26175000	22	26725000	26730000	0,255,255	74	34.8292	30.2835	36.0862	34.0141	0.000334496081071	1.87470466856e-07	0.000493654404255	0.000509206332591	4	26173750	26727500	5153.88203202	NA	NA	NA	NA	NA	26727149	26727169	CTCACCTGCAGAGGGCAGTG	n	u
45 
+22	26290000	26295000	22	26725000	26730000	0,255,255	64	28.3982	28.6944	29.6562	37.7536	0.000207107429829	0.000206048925328	0.00031599190382	0.0482820602729	2	26297500	26722500	7071.06781187	NA	NA	NA	NA	NA	26727149	26727169	CTCACCTGCAGAGGGCAGTG	n	u
46 
+22	26760000	26770000	22	27040000	27050000	0,255,255	181	101.328	83.8472	87.1106	113.455	0.000286233023047	1.81613557606e-10	2.89163470003e-10	0.000408564214978	3	26768333	27048333	7453.559925	26760578	26760598	GCAGTCACCAGATGGCAGTA	p	i	27041422	27041442	CTTACCACCAGGTGGCAGTG	n	i
47 
+22	26795000	26800000	22	26855000	26860000	0,255,255	196	70.3409	83.2495	87.764	100.103	1.7647493145e-24	1.54068113967e-14	2.3998621934e-14	9.95805208174e-07	9	26789722	26858055	27227.8905663	26794801	26794821	TAAACCACCAGATGGCATCC	p	i	26857359	26857379	GCTCACACCAGGGGGCAGCA	n	u
48 
+22	26890000	26900000	22	27040000	27050000	0,255,255	596	248.432	213.103	220.404	309.393	2.99027528952e-40	1.38415850553e-70	2.64133697385e-70	3.57521409909e-17	11	26896818	27046818	18272.5011293	26899075	26899095	GCTGCCAGCAGATGGCTCCC	p	u	27041422	27041442	CTTACCACCAGGTGGCAGTG	n	i
49 
+22	27150000	27160000	22	28400000	28410000	0,255,255	116	48.8478	45.9525	49.9819	56.6137	1.11310267338e-06	4.84722528663e-12	1.82433676885e-06	1.81929469467e-06	3	27151666	28401666	7453.559925	27152753	27152773	ACAGCCACGAGGTGTCGCCC	p	u	NA	NA	NA	NA	NA
50 
+22	28280000	28285000	22	28405000	28410000	0,255,255	220	68.0517	51.7558	81.38	54.8909	5.20250127381e-34	3.20734199388e-48	1.56332508366e-21	9.87928742387e-48	8	28285000	28399375	12135.3048993	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
51 
+22	28410000	28420000	22	29220000	29230000	0,255,255	89	32.363	35.7851	40.3955	46.7191	2.79317700845e-08	3.78880128033e-08	0.000369296756957	0.000378485039799	2	28415000	29230000	5000	NA	NA	NA	NA	NA	29225543	29225563	TTGGCCACTAGATGGCCCTG	n	u
52 
+22	28415000	28420000	22	28985000	28990000	0,255,255	62	22.056	18.2551	20.3645	29.0289	1.15057604923e-06	4.87578433763e-10	1.95363637091e-06	0.00103992695452	3	28419166	28989166	3726.7799625	NA	NA	NA	NA	NA	28990898	28990918	ATAACCCCCAGGAGGCAGTA	n	u
53 
+22	28995000	29000000	22	29225000	29230000	0,255,255	158	36.4325	37.2823	49.8961	48.6325	8.57843299117e-40	2.69820327647e-40	8.34061048411e-20	4.18660724789e-29	12	28997916	29226666	10841.3431927	28990898	28990918	ATAACCCCCAGGAGGCAGTA	n	u	29225543	29225563	TTGGCCACTAGATGGCCCTG	n	u
54 
+22	28995000	29000000	22	29435000	29440000	0,255,255	79	28.5503	27.1641	31.9889	32.4915	3.67838033366e-09	3.30707947109e-09	2.89507852481e-05	3.07518444567e-05	5	28996500	29435500	8062.2577483	28990898	28990918	ATAACCCCCAGGAGGCAGTA	n	u	29436847	29436867	TGGCCCACTAGAGGGCAGTC	n	u
55 
+22	28995000	29000000	22	29640000	29645000	0,255,255	36	13.762	10.9295	11.56	12.0698	0.0116735116903	0.000304483160243	0.000325686683948	0.000317955391554	1	28997500	29642500	0	28990898	28990918	ATAACCCCCAGGAGGCAGTA	n	u	29641698	29641718	ATGACCACCAGGTGTCACTG	n	u
56 
+22	29250000	29255000	22	29435000	29440000	0,255,255	235	72.2745	65.5839	75.7906	80.3553	1.47198523911e-40	9.17199234354e-41	2.77218154357e-40	1.26583307429e-26	15	29253166	29433833	11352.9242439	29251771	29251791	TCTAGCACTAGGGGGCAATA	p	u	29436847	29436867	TGGCCCACTAGAGGGCAGTC	n	u
57 
+22	29250000	29255000	22	29640000	29645000	0,255,255	74	25.7994	24.2192	25.5461	31.4532	2.01023222364e-07	1.9640216682e-11	3.28399197539e-07	0.000509206332591	2	29252500	29640000	2500	29251771	29251791	TCTAGCACTAGGGGGCAATA	p	u	29641698	29641718	ATGACCACCAGGTGTCACTG	n	u
58 
+22	29560000	29565000	22	29595000	29600000	0,255,255	403	199.695	179.694	197.222	188.886	3.78532180127e-16	4.15409558524e-33	5.18269104535e-16	7.54033299345e-33	7	29558928	29601785	8601.13898485	NA	NA	NA	NA	NA	29598754	29598774	TCAGCCAGTGGGTGGCAGTG	p	u
59 
+22	29560000	29565000	22	29640000	29645000	0,255,255	156	64.9079	72.3488	87.6419	89.6943	1.6713022729e-11	1.66606882493e-11	2.69353382521e-05	2.63523433349e-05	3	29555833	29640833	6871.84270936	NA	NA	NA	NA	NA	29641698	29641718	ATGACCACCAGGTGTCACTG	n	u
60 
+22	29790000	29795000	22	29920000	29925000	0,255,255	122	57.1152	55.9593	67.8105	59.4391	2.06121092736e-08	2.01746716886e-08	0.00089168164913	3.28687463985e-08	2	29792500	29920000	2500	29791125	29791145	GCGCCCACTAGAGTGCGCAC	p	u	29920622	29920642	GACCCCAGCAGAGGGAGCCC	n	u
inst/extdata/GM12878_Stat1.chr22_1-18000000.bigWig
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0 61 
deleted file mode 100644
1 62 
Binary files a/inst/extdata/GM12878_Stat1.chr22_1-18000000.bigWig and /dev/null differ
inst/extdata/GM12878_Stat1.chr22_1-30000000.bigWig
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new file mode 100644
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man/addCor.Rd
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... ... 
@@ -38,7 +38,7 @@ if (.Platform$OS.type != "windows") {
38 38
39 39 
  # use example bigWig file of ChIP-seq signals on human chromosome 22
40 40 
  exampleBigWig <- system.file("extdata",
41 
- "GM12878_Stat1.chr22_1-18000000.bigWig", package = "sevenC")
41 
+ "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")
42 42
43 43 
  # use example CTCF moitf location on human chromosome 22
44 44 
  motifGR <- sevenC::motif.hg19.CTCF.chr22
man/addCovCor.Rd
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... ... 
@@ -48,7 +48,7 @@ if (.Platform$OS.type != "windows") {
48 48
49 49 
   # use example bigWig file
50 50 
  exampleBigWig <- system.file("extdata",
51 
-     "GM12878_Stat1.chr22_1-18000000.bigWig", package = "sevenC")
51 
+     "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")
52 52
53 53 
   # add coverage from bigWig file
54 54 
   motifGR <- addCovToGR(motifGR, exampleBigWig)
man/addCovToGR.Rd
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... ... 
@@ -42,7 +42,7 @@ if (.Platform$OS.type != "windows") {
42 42
43 43 
  # use example bigWig file of ChIP-seq signals on human chromosome 22
44 44 
  exampleBigWig <- system.file("extdata",
45 
- "GM12878_Stat1.chr22_1-18000000.bigWig", package = "sevenC")
45 
+ "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")
46 46
47 47 
  # use example CTCF moitf location on human chromosome 22
48 48 
  motifGR <- sevenC::motif.hg19.CTCF.chr22
man/parseLoopsRao.Rd
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... ... 
@@ -24,7 +24,7 @@ Parse chromatin loops from Rao et al. 2014 as strict
24 24
25 25 
 # use example loop file
26 26 
 exampleLoopFile <- system.file("extdata",
27 
-  "GM12878_HiCCUPS.chr22_1-18000000.loop.txt", package = "sevenC")
27 
+  "GM12878_HiCCUPS.chr22_1-30000000.loop.txt", package = "sevenC")
28 28
29 29 
 # read loops form example file:
30 30 
 gi <- parseLoopsRao(exampleLoopFile)
man/parseLoopsTang2015.Rd
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... ... 
@@ -32,7 +32,7 @@ file is added as annotation column with colname "score".
32 32 
 }
33 33 
 \examples{
34 34 
 exampleLoopTang2015File <- system.file("extdata",
35 
-   "ChIA-PET_GM12878_Tang2015.chr22_1-18000000.clusters.txt",
35 
+   "ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt",
36 36 
    package = "sevenC")
37 37
38 38 
 gi <- parseLoopsTang2015(exampleLoopTang2015File)
tests/testthat/test-interaction.R
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... ... 
@@ -153,7 +153,7 @@ test_that("coverage is added to gi on small example dataset", {
153 153 
 test_that("addCovCor works with chr22 example data", {
154 154
155 155 
   exampleBigWig <- system.file("extdata",
156 
-                               "GM12878_Stat1.chr22_1-18000000.bigWig",
156 
+                               "GM12878_Stat1.chr22_1-30000000.bigWig",
157 157 
                                package = "sevenC")
158 158
159 159 
   # use internal motif data
... ... 
@@ -234,7 +234,7 @@ test_that("interactions can be annotated with Hi-C loops", {
234 234 
   # parse loops from internal data
235 235 
   exampleLoopFile <- system.file(
236 236 
     "extdata",
237 
-    "GM12878_HiCCUPS.chr22_1-18000000.loop.txt",
237 
+    "GM12878_HiCCUPS.chr22_1-30000000.loop.txt",
238 238 
     package = "sevenC")
239 239
240 240 
   loopGI <- parseLoopsRao(exampleLoopFile, seqinfo = seqinfo(gi))
tests/testthat/test-parseChIP-seq.R
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... ... 
@@ -1,6 +1,6 @@
1 1 
 context("parseChIP-seq")
2 2
3 
-exampleBigWig <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
3 
+exampleBigWig <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
4 4 
                              package = "sevenC")
5 5
6 6 
 toySeqInfo <- Seqinfo(seqnames = c("chr1", "chr22"),
... ... 
@@ -11,8 +11,8 @@ toySeqInfo <- Seqinfo(seqnames = c("chr1", "chr22"),
11 11 
 exampleGR <- GRanges(
12 12 
   rep("chr22", 3),
13 13 
   IRanges(
14 
-    18000000 - c(1000, 500, 100),
15 
-    18000000 - c(991, 491, 91)
14 
+    30000000 - c(1000, 500, 100),
15 
+    30000000 - c(991, 491, 91)
16 16 
   ),
17 17 
   seqinfo = Seqinfo(seqnames = "chr22",
18 18 
                                   seqlengths = 10^8,
tests/testthat/test-parseInteractions.R
History View file @ 3b17dcb
... ... 
@@ -2,7 +2,7 @@ context("parseInteractions")
2 2
3 3
4 4 
 exampleLoopFile <- system.file("extdata",
5 
-                               "GM12878_HiCCUPS.chr22_1-18000000.loop.txt",
5 
+                               "GM12878_HiCCUPS.chr22_1-30000000.loop.txt",
6 6 
                                package = "sevenC")
7 7
8 8
... ... 
@@ -36,7 +36,7 @@ test_that("parseLoopsTang2015 works with example file", {
36 36
37 37 
   exampleLoopTang2015File <- system.file(
38 38 
     "extdata",
39 
-    "ChIA-PET_GM12878_Tang2015.chr22_1-18000000.clusters.txt",
39 
+    "ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt",
40 40 
     package = "sevenC")
41 41
42 42 
   gi <- parseLoopsTang2015(exampleLoopTang2015File)
vignettes/sevenC.Rmd
History View file @ 3b17dcb
... ... 
@@ -88,7 +88,7 @@ gi <- prepareCisPairs(motifs)
88 88 
 ```{r eval = FALSE, echo = TRUE}
89 89
90 90 
 # use example ChIP-seq bigWig file
91 
-bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
91 
+bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
92 92 
   package = "sevenC")
93 93
94 94 
 # add ChIP-seq coverage and compute correaltion at motif pairs
... ... 
@@ -105,7 +105,7 @@ if (.Platform$OS.type == 'windows') {
105 105
106 106 
 } else {
107 107 
   # use example ChIP-seq bigWig file
108 
-  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
108 
+  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
109 109 
     package = "sevenC")
110 110
111 111 
   # add ChIP-seq coverage and compute correaltion at motif pairs
... ... 
@@ -153,7 +153,7 @@ the `r BiocStyle::Biocpkg("sevenC")` package. The full file can be downloaded fr
153 153
154 154 
 ```{r}
155 155 
 # use example ChIP-seq bigWig file
156 
-bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
156 
+bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
157 157 
   package = "sevenC")
158 158 
 ```
159 159
... ... 
@@ -253,7 +253,7 @@ First, we need to build the pairs of motifs as candidates and add the ChIP-seq d
253 253 
 motifs <- motif.hg19.CTCF.chr22
254 254
255 255 
 # use example ChIP-seq coverage file
256 
-bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
256 
+bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
257 257 
   package = "sevenC")
258 258
259 259 
 # add ChIP-seq coverage
... ... 
@@ -275,7 +275,7 @@ if (.Platform$OS.type == 'windows') {
275 275 
   motifs <- motif.hg19.CTCF.chr22
276 276
277 277 
   # use example ChIP-seq coverage file
278 
-  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
278 
+  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
279 279 
     package = "sevenC")
280 280
281 281 
   # add ChIP-seq coverage
... ... 
@@ -296,7 +296,7 @@ An example file with loops on chromosome 22 is provided with the `r BiocStyle::B
296 296 
 ```{r, message = FALSE}
297 297 
 # parse known loops
298 298 
 knownLoopFile <- system.file("extdata",
299 
-  "GM12878_HiCCUPS.chr22_1-18000000.loop.txt", package = "sevenC")
299 
+  "GM12878_HiCCUPS.chr22_1-30000000.loop.txt", package = "sevenC")
300 300
301 301 
 knownLoops <- parseLoopsRao(knownLoopFile)
302 302 
 ```