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1 ## How to execute this tool
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2 # $Rscript GSEA.R --input ranked_genes_list.rnk --input Mus_musculus_GSEA_GO_sets_all_symbols_highquality_April_2015.gmt
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3 # --output GSEA_results.txt --output
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4
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5 # Send R errors to stderr
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6 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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7
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8 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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9 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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10
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11 # Import library
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12 library("getopt")
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13 library("fgsea")
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14 library("Rcpp")
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15
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16 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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17
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18 # Take in trailing command line arguments
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19 args <- commandArgs(trailingOnly = TRUE)
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20
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21 # Get options using the spec as defined by the enclosed list
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22 # Options are read from the default: commandArgs(TRUE)
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23 option_specification = matrix(c(
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24 'input1', 'i1', 2, 'character',
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25 'input2', 'i2', 2, 'character',
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26 'output', 'o', 2, 'character'
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27 ), byrow = TRUE, ncol = 4);
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28
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29 # Parse options
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30 options = getopt(option_specification);
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31
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32 # Print options to stderr for debugging
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33 # cat("\n input: ", options$input1)
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34 # cat("\n input: ", options$input2)
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35 # cat("\n output: ", options$output)
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36
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37 # Rank file
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38 ranks <- read.table(options$input1, header=F, colClasses = c("character", "numeric"))
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39 ranks <- setNames(ranks[,2], ranks[,1])
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40
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41 # Pathways database
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42 pathways <- gmtPathways(options$input2)
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43
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44 # running analysis
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45 fgseaRes <- fgsea(pathways, ranks, minSize=10, maxSize=500, nperm=1000)
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46 res <- as.data.frame(fgseaRes[order(pval), ], stringsAsFactors = F)
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47
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48 # save results
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49 write.table(x = res[,1:7], file = options$output, quote = F, row.names = F, sep = "\t")
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50 #
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51 # topPathwaysUp <- fgseaRes[ES > 0][head(order(pval), n=10), pathway]
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52 # topPathwaysDown <- fgseaRes[ES < 0][head(order(pval), n=10), pathway]
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53 # topPathways <- c(topPathwaysUp, rev(topPathwaysDown))
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54 #
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55 # pdf(paste0(options$output, ".pdf"), width = 8.5, height = 11)
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56 # plotGseaTable(pathways[topPathways], ranks, fgseaRes,gseaParam = 0.5)
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57 # z <- dev.off() |
