Mercurial > repos > iuc > multigsea

annotate multiGSEA.R @ 1:e48b10ce08b8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
author iuc
date Wed, 21 Feb 2024 15:41:52 +0000
parents 28e29a3d0eda
children
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28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
iuc
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1 library(multiGSEA,
1
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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2 quietly = TRUE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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3 warn.conflicts = FALSE
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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4 )
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iuc
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5 library(argparse, quietly = TRUE, warn.conflicts = FALSE)
28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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7 ################################################################################
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8 ### Input Processing
28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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9 ################################################################################
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12 # Collect arguments from command line
28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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13 parser <- ArgumentParser(description = "multiGSEA R script")
28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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14
1
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15 parser$add_argument("--transcriptomics",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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16 required = FALSE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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17 help = "Transcriptomics data"
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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18 )
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28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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19 parser$add_argument(
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20 "--transcriptome_ids",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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21 required = FALSE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
iuc
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22 help = "Transcriptomics ids",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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23 default = "SYMBOL"
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24 )
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e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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25 parser$add_argument("--proteomics",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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26 required = FALSE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
iuc
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27 help = "Proteomics data"
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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28 )
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28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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29 parser$add_argument(
1
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30 "--proteome_ids",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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31 required = FALSE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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32 help = "Proteomics ids",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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33 default = "SYMBOL"
0
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34 )
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35 parser$add_argument("--metabolomics",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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36 required = FALSE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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37 help = "Metabolomics data"
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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38 )
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28e29a3d0eda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
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39 parser$add_argument(
1
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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40 "--metabolome_ids",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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41 required = FALSE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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42 help = "Metabolomics ids",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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43 default = "HMDB"
0
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44 )
1
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45 parser$add_argument("--organism",
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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46 required = TRUE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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47 help = "Organism"
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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48 )
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49 parser$add_argument("--combine_pvalues",
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50 required = TRUE,
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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51 help = "Combine p-values method"
e48b10ce08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878
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52 )
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53 parser$add_argument("--padj_method",
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54 required = TRUE,
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55 help = "P-adjustment method"
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56 )
0
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57 parser$add_argument("--databases",
1
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58 required = TRUE,
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59 help = "Pathway databases"
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60 )
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62 args <- parser$parse_args()
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64 ## ----Load library-------------------------------------------------------------
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65
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66 organism_mapping <- c(
1
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67 "hsapiens" = "org.Hs.eg.db",
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68 "mmusculus" = "org.Mm.eg.db",
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69 "rnorvegicus" = "org.Rn.eg.db",
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70 "cfamiliaris" = "org.Cf.eg.db",
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71 "btaurus" = "org.Bt.eg.db",
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72 "sscrofa" = "org.Ss.eg.db",
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73 "ggallus" = "org.Gg.eg.db",
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74 "drerio" = "org.Xl.eg.db",
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75 "xlaevis" = "org.Dr.eg.db",
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76 "dmelanogaster" = "org.Dm.eg.db",
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77 "celegans" = "org.Ce.eg.db"
0
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78 )
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80 library(organism_mapping[args$organism], character.only = TRUE)
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83 ## ----Load omics data----------------------------------------------------------
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84
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85 layer <- c()
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86
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87 if (!is.null(args$transcriptomics)) {
1
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88 transcriptome <- read.csv(
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89 args$transcriptomics,
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90 header = TRUE,
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91 sep = "\t",
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92 dec = "."
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93 )
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94 layer <- append(layer, "transcriptome")
0
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95 }
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96
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97 if (!is.null(args$proteomics)) {
1
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98 proteome <- read.csv(args$proteomics,
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99 header = TRUE,
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100 sep = "\t",
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101 dec = "."
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102 )
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103 layer <- append(layer, "proteome")
0
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104 }
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105
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106 if (!is.null(args$metabolomics)) {
1
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107 metabolome <- read.csv(args$metabolomics,
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108 header = TRUE,
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109 sep = "\t",
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110 dec = "."
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111 )
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112 layer <- append(layer, "metabolome")
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113 }
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114
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115 ## ----rank_features------------------------------------------------------------
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116
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117 # create data structure
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118 omics_data <- initOmicsDataStructure(layer)
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119
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120 ## add transcriptome layer
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121 if (!is.null(args$transcriptomics)) {
1
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122 omics_data$transcriptome <- rankFeatures(
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123 transcriptome$logFC,
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124 transcriptome$pValue
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125 )
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126 names(omics_data$transcriptome) <- transcriptome$Symbol
0
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127 }
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128
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129 ## add proteome layer
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130 if (!is.null(args$proteomics)) {
1
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131 omics_data$proteome <- rankFeatures(proteome$logFC, proteome$pValue)
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132 names(omics_data$proteome) <- proteome$Symbol
0
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133 }
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134
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135 ## add metabolome layer
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136 ## HMDB features have to be updated to the new HMDB format
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137 if (!is.null(args$metabolomics)) {
1
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138 omics_data$metabolome <-
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139 rankFeatures(metabolome$logFC, metabolome$pValue)
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140 names(omics_data$metabolome) <- metabolome$HMDB
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141 names(omics_data$metabolome) <- gsub(
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142 "HMDB", "HMDB00",
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143 names(omics_data$metabolome)
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144 )
0
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145 }
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146
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147
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148 ## remove NA's and sort feature ranks
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149 omics_data <- lapply(omics_data, function(vec) {
1
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150 sort(vec[!is.na(vec)])
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151 })
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152
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153 ## ----Pathway definitions------------------------------------------------------
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154
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155 pathways <-
1
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156 getMultiOmicsFeatures(
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157 dbs = unlist(strsplit(args$databases, ",", fixed = TRUE)),
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158 layer = layer,
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159 returnTranscriptome = args$transcriptome_ids,
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160 returnProteome = args$proteome_ids,
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161 returnMetabolome = args$metabolome_ids,
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162 organism = args$organism,
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163 useLocal = FALSE
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164 )
0
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165
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166 ## ----calculate enrichment-----------------------------------------------------
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167
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168 enrichment_scores <-
1
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169 multiGSEA(pathways, omics_data)
0
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170
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171 ## ----combine_pvalues----------------------------------------------------------
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172
1
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173 df <- extractPvalues(
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174 enrichmentScores = enrichment_scores,
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175 pathwayNames = names(pathways[[1]])
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176 )
0
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177
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178 df$combined_pval <-
1
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179 combinePvalues(df, method = args$combine_pvalues)
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180 df$combined_padj <-
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181 p.adjust(df$combined_pval, method = args$padj_method)
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182
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183 df <- cbind(data.frame(pathway = names(pathways[[1]])), df)
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184
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185 ## ----Write output-------------------------------------------------------------
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186
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187 write.table(
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188 df,
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189 file = "results.tsv",
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190 quote = FALSE,
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191 sep = "\t",
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192 col.names = TRUE,
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193 row.names = FALSE
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194 )