1. GSVA
  2. NAMESPACE
Browse code

changing function viewReduce for gridReduce from DelayedArray

pablo-rodr-bio2 authored on 18/11/2021 08:36:13
Showing 1 changed files
NAMESPACE
History View file @ f618fa48
... ... 
@@ -58,7 +58,7 @@ importFrom(DelayedArray, rowAutoGrid,
58 58 
 			  defaultAutoGrid,
59 59 
 			  currentBlockId,
60 60 
 			  read_block,
61 
-			  viewportReduce,
61 
+			  gridReduce,
62 62 
 			  write_block,
63 63 
 			  close,
64 64 
 			  t)
Browse code

Replaced fastmatch::fmatch() by IRanges::match,CharacterList-method after disscussion at https://github.com/rcastelo/GSVA/issues/39

Robert Castelo authored on 03/02/2021 16:09:12
Showing 1 changed files
NAMESPACE
History View file @ 0093798f
... ... 
@@ -18,6 +18,7 @@ importMethodsFrom(Biobase, featureNames,
18 18
19 19 
 importMethodsFrom(S4Vectors, metadata,
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                              "metadata<-")
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+importMethodsFrom(IRanges, match)
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22 23 
 importMethodsFrom(SummarizedExperiment, assays,
23 24 
                                         colData)
... ... 
@@ -40,6 +41,7 @@ importFrom(utils, installed.packages,
40 41 
                   read.csv,
41 42 
                   write.csv)
42 43 
 importFrom(S4Vectors, SimpleList)
44 
+importFrom(IRanges, CharacterList)
43 45 
 importFrom(GSEABase, AnnoOrEntrezIdentifier,
44 46 
                      mapIdentifiers,
45 47 
                      getGmt)
Browse code

Fixing a bug in delayed zscore method and getting back tests

pablo-rodr-bio2 authored on 25/01/2021 17:51:59
Showing 1 changed files
NAMESPACE
History View file @ 1a9a4353
... ... 
@@ -1,7 +1,6 @@
1 1 
 useDynLib(GSVA)
2 2
3 3 
 import(methods)
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-import(BiocGenerics)
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6 5 
 importClassesFrom(Biobase, ExpressionSet)
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 importClassesFrom(SummarizedExperiment, SummarizedExperiment)
... ... 
@@ -33,7 +32,8 @@ importMethodsFrom(BiocParallel, bpiterate,
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34 33 
 importFrom(graphics, plot)
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 importFrom(stats, ecdf,
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-                  na.omit)
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+                  na.omit,
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+                  sd)
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 importFrom(utils, installed.packages,
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                   setTxtProgressBar,
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                   txtProgressBar,
... ... 
@@ -58,8 +58,10 @@ importFrom(DelayedArray, rowAutoGrid,
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 			  read_block,
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 			  viewportReduce,
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 			  write_block,
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-			  close)
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-importFrom(HDF5Array, HDF5RealizationSink)
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+			  close,
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+			  t)
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+importFrom(HDF5Array, HDF5RealizationSink,
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+                      writeHDF5Array)
63 65 
 importFrom(DelayedMatrixStats, rowSds)
64 66 
 importFrom(BiocSingular, runRandomSVD)
65 67
Browse code

adding runRandomSVD() to plageDelayed method for better use of on-disk backend

pablo-rodr-bio2 authored on 11/01/2021 11:22:49
Showing 1 changed files
NAMESPACE
History View file @ 1e5b296a
... ... 
@@ -61,6 +61,7 @@ importFrom(DelayedArray, rowAutoGrid,
61 61 
 			  close)
62 62 
 importFrom(HDF5Array, HDF5RealizationSink)
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 importFrom(DelayedMatrixStats, rowSds)
64 
+importFrom(BiocSingular, runRandomSVD)
64 65
65 66 
 exportMethods(gsva,
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               filterGeneSets,
Browse code

added delayed support for ssgsea method

pablo-rodr-bio2 authored on 21/12/2020 20:59:05
Showing 1 changed files
NAMESPACE
History View file @ 4d99d34c
... ... 
@@ -53,6 +53,7 @@ importFrom(SingleCellExperiment, SingleCellExperiment)
53 53 
 importFrom(sparseMatrixStats, colRanks)
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 importFrom(DelayedArray, rowAutoGrid,
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 			  colAutoGrid,
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+			  defaultAutoGrid,
56 57 
 			  currentBlockId,
57 58 
 			  read_block,
58 59 
 			  viewportReduce,
Browse code

added ssgsea method for DelayedArray

pablo-rodr-bio2 authored on 15/12/2020 13:14:39
Showing 1 changed files
NAMESPACE
History View file @ ce958b8e
... ... 
@@ -52,6 +52,10 @@ importFrom(BiocParallel, SerialParam,
52 52 
 importFrom(SingleCellExperiment, SingleCellExperiment)
53 53 
 importFrom(sparseMatrixStats, colRanks)
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 importFrom(DelayedArray, rowAutoGrid,
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+			  colAutoGrid,
56 
+			  currentBlockId,
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+			  read_block,
58 
+			  viewportReduce,
55 59 
 			  write_block,
56 60 
 			  close)
57 61 
 importFrom(HDF5Array, HDF5RealizationSink)
Browse code

added hdf5 support for plage method

pablo-rodr-bio2 authored on 20/11/2020 18:38:41
Showing 1 changed files
NAMESPACE
History View file @ 9136daba
... ... 
@@ -8,6 +8,8 @@ importClassesFrom(SummarizedExperiment, SummarizedExperiment)
8 8 
 importClassesFrom(GSEABase, GeneSetCollection)
9 9 
 importClassesFrom(SingleCellExperiment, SingleCellExperiment)
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 importClassesFrom(Matrix, dgCMatrix)
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+importClassesFrom(DelayedArray, DelayedArray)
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+importClassesFrom(HDF5Array, HDF5Array)
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12 14 
 importMethodsFrom(Biobase, featureNames,
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                            phenoData,
... ... 
@@ -48,8 +50,12 @@ importFrom(BiocParallel, SerialParam,
48 50 
                          multicoreWorkers,
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                          bpnworkers)
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 importFrom(SingleCellExperiment, SingleCellExperiment)
51 
-importFrom(BiocSingular, runExactSVD)
52 53 
 importFrom(sparseMatrixStats, colRanks)
54 
+importFrom(DelayedArray, rowAutoGrid,
55 
+			  write_block,
56 
+			  close)
57 
+importFrom(HDF5Array, HDF5RealizationSink)
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+importFrom(DelayedMatrixStats, rowSds)
53 59
54 60 
 exportMethods(gsva,
55 61 
               filterGeneSets,
Browse code

adding sparse support to method ssgsea

pablo-rodr-bio2 authored on 13/11/2020 12:45:26
Showing 1 changed files
NAMESPACE
History View file @ 6e254afc
... ... 
@@ -49,6 +49,7 @@ importFrom(BiocParallel, SerialParam,
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                          bpnworkers)
50 50 
 importFrom(SingleCellExperiment, SingleCellExperiment)
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 importFrom(BiocSingular, runExactSVD)
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+importFrom(sparseMatrixStats, colRanks)
52 53
53 54 
 exportMethods(gsva,
54 55 
               filterGeneSets,
Browse code

adding sparse support to method plage

pablo-rodr-bio2 authored on 10/11/2020 11:04:28
Showing 1 changed files
NAMESPACE
History View file @ 5166605f
... ... 
@@ -29,8 +29,6 @@ importMethodsFrom(BiocParallel, bpiterate,
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                                 bplapply,
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                                 "bpprogressbar<-")
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-importMethodsFrom(BiocSingular, runExactSVD)
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-
34 32 
 importFrom(graphics, plot)
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 importFrom(stats, ecdf,
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                   na.omit)
... ... 
@@ -50,6 +48,7 @@ importFrom(BiocParallel, SerialParam,
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                          multicoreWorkers,
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                          bpnworkers)
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 importFrom(SingleCellExperiment, SingleCellExperiment)
51 
+importFrom(BiocSingular, runExactSVD)
53 52
54 53 
 exportMethods(gsva,
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               filterGeneSets,
Browse code

adding dgCMatrix support to method plage

pablo-rodr-bio2 authored on 09/11/2020 11:11:55
Showing 1 changed files
NAMESPACE
History View file @ b4f13708
... ... 
@@ -29,6 +29,8 @@ importMethodsFrom(BiocParallel, bpiterate,
29 29 
                                 bplapply,
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                                 "bpprogressbar<-")
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32 
+importMethodsFrom(BiocSingular, runExactSVD)
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+
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 importFrom(graphics, plot)
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 importFrom(stats, ecdf,
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                   na.omit)
Browse code

adding dgCMatrix/list support

pablo-rodr-bio2 authored on 02/11/2020 18:20:08
Showing 1 changed files
NAMESPACE
History View file @ 763cb48d
... ... 
@@ -7,6 +7,7 @@ importClassesFrom(Biobase, ExpressionSet)
7 7 
 importClassesFrom(SummarizedExperiment, SummarizedExperiment)
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 importClassesFrom(GSEABase, GeneSetCollection)
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 importClassesFrom(SingleCellExperiment, SingleCellExperiment)
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+importClassesFrom(Matrix, dgCMatrix)
10 11
11 12 
 importMethodsFrom(Biobase, featureNames,
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                            phenoData,
Browse code

adding SingleCellExperiment support

pablo-rodr-bio2 authored on 29/10/2020 11:43:14
Showing 1 changed files
NAMESPACE
History View file @ e48a4a3c
... ... 
@@ -6,6 +6,7 @@ import(BiocGenerics)
6 6 
 importClassesFrom(Biobase, ExpressionSet)
7 7 
 importClassesFrom(SummarizedExperiment, SummarizedExperiment)
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 importClassesFrom(GSEABase, GeneSetCollection)
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+importClassesFrom(SingleCellExperiment, SingleCellExperiment)
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 importMethodsFrom(Biobase, featureNames,
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                            phenoData,
... ... 
@@ -45,6 +46,7 @@ importFrom(BiocParallel, SerialParam,
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                          MulticoreParam,
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                          multicoreWorkers,
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                          bpnworkers)
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+importFrom(SingleCellExperiment, SingleCellExperiment)
48 50
49 51 
 exportMethods(gsva,
50 52 
               filterGeneSets,
Browse code

Removed parallelization throughout gene sets in the internal zscore() function. Moved shiny app dependencies to suggests.

Robert Castelo authored on 01/09/2020 17:18:39
Showing 1 changed files
NAMESPACE
History View file @ 5e5eb749
... ... 
@@ -2,7 +2,6 @@ useDynLib(GSVA)
2 2
3 3 
 import(methods)
4 4 
 import(BiocGenerics)
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-import(shiny)
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 importClassesFrom(Biobase, ExpressionSet)
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 importClassesFrom(SummarizedExperiment, SummarizedExperiment)
... ... 
@@ -46,7 +45,6 @@ importFrom(BiocParallel, SerialParam,
46 45 
                          MulticoreParam,
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                          multicoreWorkers,
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                          bpnworkers)
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-importFrom(shinythemes, shinytheme)
50 48
51 49 
 exportMethods(gsva,
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               filterGeneSets,
Browse code

Added methods to take expression data in a SummarizedExperiment object.

Robert Castelo authored on 16/12/2019 11:46:25
Showing 1 changed files
NAMESPACE
History View file @ 8de45582
... ... 
@@ -6,16 +6,20 @@ import(shiny)
6 6
7 7 
 importClassesFrom(Biobase, ExpressionSet)
8 8 
 importClassesFrom(SummarizedExperiment, SummarizedExperiment)
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-importClassesFrom(SingleCellExperiment, SingleCellExperiment)
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 importClassesFrom(GSEABase, GeneSetCollection)
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 importMethodsFrom(Biobase, featureNames,
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                            phenoData,
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                            experimentData,
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-                           esApply,
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                            exprs,
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                            annotation)
18 16
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+importMethodsFrom(S4Vectors, metadata,
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+                             "metadata<-")
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+
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+importMethodsFrom(SummarizedExperiment, assays,
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+                                        colData)
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+
19 23 
 importMethodsFrom(GSEABase, geneIds,
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                             incidence)
21 25
... ... 
@@ -27,13 +31,16 @@ importMethodsFrom(BiocParallel, bpiterate,
27 31 
 importFrom(graphics, plot)
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 importFrom(stats, ecdf,
29 33 
                   na.omit)
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-importFrom(utils, setTxtProgressBar,
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+importFrom(utils, installed.packages,
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+                  setTxtProgressBar,
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                   txtProgressBar,
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                   read.csv,
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                   write.csv)
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+importFrom(S4Vectors, SimpleList)
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 importFrom(GSEABase, AnnoOrEntrezIdentifier,
35 41 
                      mapIdentifiers,
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                      getGmt)
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+importFrom(SummarizedExperiment, SummarizedExperiment)
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 importFrom(parallel, splitIndices)
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 importFrom(BiocParallel, SerialParam,
39 46 
                          MulticoreParam,
Browse code

Removed the parallel.type argument from gsva(). Updated manual page.

Robert Castelo authored on 10/12/2019 13:09:53
Showing 1 changed files
NAMESPACE
History View file @ 5fa44af1
... ... 
@@ -5,6 +5,8 @@ import(BiocGenerics)
5 5 
 import(shiny)
6 6
7 7 
 importClassesFrom(Biobase, ExpressionSet)
8 
+importClassesFrom(SummarizedExperiment, SummarizedExperiment)
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+importClassesFrom(SingleCellExperiment, SingleCellExperiment)
8 10 
 importClassesFrom(GSEABase, GeneSetCollection)
9 11
10 12 
 importMethodsFrom(Biobase, featureNames,
... ... 
@@ -37,7 +39,6 @@ importFrom(BiocParallel, SerialParam,
37 39 
                          MulticoreParam,
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                          multicoreWorkers,
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                          bpnworkers)
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-importFrom(geneplotter, multidensity)
41 42 
 importFrom(shinythemes, shinytheme)
42 43
43 44 
 exportMethods(gsva,
Browse code

Updated the implementation of parallel calculations to use BiocParallel.

Robert Castelo authored on 29/11/2019 18:40:31
Showing 1 changed files
NAMESPACE
History View file @ 262a4397
... ... 
@@ -18,7 +18,9 @@ importMethodsFrom(GSEABase, geneIds,
18 18 
                             incidence)
19 19
20 20 
 importMethodsFrom(BiocParallel, bpiterate,
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-                                "bpworkers<-")
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+                                "bpworkers<-",
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+                                bplapply,
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+                                "bpprogressbar<-")
22 24
23 25 
 importFrom(graphics, plot)
24 26 
 importFrom(stats, ecdf,
Browse code

Added the possibility of doing the ECDF estimation using parallel calculations.

Robert Castelo authored on 29/11/2019 12:12:34
Showing 1 changed files
NAMESPACE
History View file @ 5df67ea4
... ... 
@@ -9,11 +9,17 @@ importClassesFrom(GSEABase, GeneSetCollection)
9 9
10 10 
 importMethodsFrom(Biobase, featureNames,
11 11 
                            phenoData,
12 
-                           experimentData)
12 
+                           experimentData,
13 
+                           esApply,
14 
+                           exprs,
15 
+                           annotation)
13 16
14 17 
 importMethodsFrom(GSEABase, geneIds,
15 18 
                             incidence)
16 19
20 
+importMethodsFrom(BiocParallel, bpiterate,
21 
+                                "bpworkers<-")
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+
17 23 
 importFrom(graphics, plot)
18 24 
 importFrom(stats, ecdf,
19 25 
                   na.omit)
... ... 
@@ -21,11 +27,14 @@ importFrom(utils, setTxtProgressBar,
21 27 
                   txtProgressBar,
22 28 
                   read.csv,
23 29 
                   write.csv)
24 
-importFrom(Biobase, exprs,
25 
-                    annotation)
26 30 
 importFrom(GSEABase, AnnoOrEntrezIdentifier,
27 31 
                      mapIdentifiers,
28 32 
                      getGmt)
33 
+importFrom(parallel, splitIndices)
34 
+importFrom(BiocParallel, SerialParam,
35 
+                         MulticoreParam,
36 
+                         multicoreWorkers,
37 
+                         bpnworkers)
29 38 
 importFrom(geneplotter, multidensity)
30 39 
 importFrom(shinythemes, shinytheme)
31 40
Browse code

Added first version of a GSVA shiny app.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@130609 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Castelo authored on 22/06/2017 12:53:26
Showing 1 changed files
NAMESPACE
History View file @ dfe03f19
... ... 
@@ -2,6 +2,7 @@ useDynLib(GSVA)
2 2
3 3 
 import(methods)
4 4 
 import(BiocGenerics)
5 
+import(shiny)
5 6
6 7 
 importClassesFrom(Biobase, ExpressionSet)
7 8 
 importClassesFrom(GSEABase, GeneSetCollection)
... ... 
@@ -17,12 +18,19 @@ importFrom(graphics, plot)
17 18 
 importFrom(stats, ecdf,
18 19 
                   na.omit)
19 20 
 importFrom(utils, setTxtProgressBar,
20 
-                  txtProgressBar)
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-importFrom(Biobase, exprs)
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-importFrom(Biobase, annotation)
23 
-importFrom(GSEABase, AnnoOrEntrezIdentifier)
24 
-importFrom(GSEABase, mapIdentifiers)
21 
+                  txtProgressBar,
22 
+                  read.csv,
23 
+                  write.csv)
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+importFrom(Biobase, exprs,
25 
+                    annotation)
26 
+importFrom(GSEABase, AnnoOrEntrezIdentifier,
27 
+                     mapIdentifiers,
28 
+                     getGmt)
29 
+importFrom(geneplotter, multidensity)
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+importFrom(shinythemes, shinytheme)
25 31
26 
-exportMethods("gsva",
27 
-              "filterGeneSets",
28 
-              "computeGeneSetsOverlap")
32 
+exportMethods(gsva,
33 
+              filterGeneSets,
34 
+              computeGeneSetsOverlap)
35 
+
36 
+export(igsva)
Browse code

Fixed NAMESPACE and updated documentation on the rnaseq argument of the main function gsva().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@128904 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Castelo authored on 19/04/2017 20:44:29
Showing 1 changed files
NAMESPACE
History View file @ 9fb749c5
... ... 
@@ -5,6 +5,19 @@ import(BiocGenerics)
5 5
6 6 
 importClassesFrom(Biobase, ExpressionSet)
7 7 
 importClassesFrom(GSEABase, GeneSetCollection)
8 
+
9 
+importMethodsFrom(Biobase, featureNames,
10 
+                           phenoData,
11 
+                           experimentData)
12 
+
13 
+importMethodsFrom(GSEABase, geneIds,
14 
+                            incidence)
15 
+
16 
+importFrom(graphics, plot)
17 
+importFrom(stats, ecdf,
18 
+                  na.omit)
19 
+importFrom(utils, setTxtProgressBar,
20 
+                  txtProgressBar)
8 21 
 importFrom(Biobase, exprs)
9 22 
 importFrom(Biobase, annotation)
10 23 
 importFrom(GSEABase, AnnoOrEntrezIdentifier)
Browse code

Fixed bug when input object is ExpressionSet. Now instead of replacing expression values via exprs() a new ExpressionSet object is instantiated

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@85470 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Castelo authored on 13/01/2014 09:36:56
Showing 1 changed files
NAMESPACE
History View file @ 16a8c25c
... ... 
@@ -1,6 +1,8 @@
1 1 
 useDynLib(GSVA)
2 2
3 3 
 import(methods)
4 
+import(BiocGenerics)
5 
+
4 6 
 importClassesFrom(Biobase, ExpressionSet)
5 7 
 importClassesFrom(GSEABase, GeneSetCollection)
6 8 
 importFrom(Biobase, exprs)
Browse code

Fixed the matching of Entrez-based ExpressionSet objects to GeneSetCollection objects by using GSEABase >= 1.17.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@64337 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Castelo authored on 23/03/2012 11:04:50
Showing 1 changed files
NAMESPACE
History View file @ 84ad4e67
... ... 
@@ -1,10 +1,12 @@
1 1 
 useDynLib(GSVA)
2 2
3 3 
 import(methods)
4 
-importClassesFrom(Biobase)
5 
-importClassesFrom(GSEABase)
4 
+importClassesFrom(Biobase, ExpressionSet)
5 
+importClassesFrom(GSEABase, GeneSetCollection)
6 6 
 importFrom(Biobase, exprs)
7 7 
 importFrom(Biobase, annotation)
8 
+importFrom(GSEABase, AnnoOrEntrezIdentifier)
9 
+importFrom(GSEABase, mapIdentifiers)
8 10
9 11 
 exportMethods("gsva",
10 12 
               "filterGeneSets",
Browse code

Added the GSVA package to the repository

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@54777 bc3139a8-67e5-0310-9ffc-ced21a209358

Chao-Jen Wong authored on 13/04/2011 04:33:14
Showing 1 changed files
NAMESPACE
History View file @ 919e21e0
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,11 @@
1 
+useDynLib(GSVA)
2 
+
3 
+import(methods)
4 
+importClassesFrom(Biobase)
5 
+importClassesFrom(GSEABase)
6 
+importFrom(Biobase, exprs)
7 
+importFrom(Biobase, annotation)
8 
+
9 
+exportMethods("gsva",
10 
+              "filterGeneSets",
11 
+              "computeGeneSetsOverlap")