# HG changeset patch # User artbio # Date 1560698832 14400 # Node ID 3362f5b5099f4ca714e6e73a1cece2eacc073e8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc-filter_genes commit 5e0f0621810b4e523005545fcd173ea18637693d diff -r 000000000000 -r 3362f5b5099f filter_genes.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_genes.R Sun Jun 16 11:27:12 2019 -0400 @@ -0,0 +1,79 @@ +# ######################## +# filter genes # +# ######################## + +# Filter out low expressed genes + +# Example of command (used for generate output file) : +# Rscript filter_genes.R -f -o + +# load packages that are provided in the conda env +options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +library(optparse) + +# Arguments +option_list = list( + make_option( + c("-f", "--input"), + default = NA, + type = 'character', + help = "Input file that contains count values to filter" + ), + make_option( + c("-s", "--sep"), + default = '\t', + type = 'character', + help = "File separator [default : '%default' ]" + ), + make_option( + c("-c", "--colnames"), + default = TRUE, + type = 'logical', + help = "first line is a header [default : '%default' ]" + ), + make_option( + "--detection", + default = 0.05, + type = 'numeric', + help = "Include genes with detected expression in at least \ + this fraction of cells [default : '%default' ]" + ), + make_option( + c("-o", "--output"), + default = NA, + type = 'character', + help = "Output name [default : '%default' ]" + ) +) + +opt = parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) +if (opt$sep == "tab") {opt$sep = "\t"} +if (opt$sep == "comma") {opt$sep = ","} + +# Open files +data.counts <- read.table( + opt$input, + h = opt$colnames, + row.names = 1, + sep = opt$sep, + check.names = F +) + +# Search for genes that are expressed in a certain percent of cells +kept_genes <- rowSums(data.counts != 0) > (opt$detection * ncol(data.counts)) + +# Filter matrix +data.counts <- data.counts[kept_genes,] + +# Save filtered matrix +write.table( + data.counts, + opt$output, + sep = "\t", + quote = F, + col.names = T, + row.names = T +) \ No newline at end of file diff -r 000000000000 -r 3362f5b5099f filter_genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_genes.xml Sun Jun 16 11:27:12 2019 -0400 @@ -0,0 +1,86 @@ + + which are detected in less that a given fraction of the libraries + + r-optparse + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +The tools takes a table of _normalized_ gene expression values +(i.e. log2(CPM+1), TPM, RPK, etc...) from single cell RNAseq sequencing libraries (columns) +and filters out genes (rows) that are detected in less than the specified fraction of libraries. + +A TSV gene expression table for genes that passed the filter is returned. + +**Input** + +A table of comma (csv) or tabulation (tsv) separated values of _normalized_ gene expressions, +i.e. log2(CPM+1), TPM, RPK, etc... +Gene names should be in the first column and cell names should be in the first row. +Note that in a number of a csv files, header of the gene column is omitted, resulting in +a first row with one item less than in other rows. Although this is not recommended, the tool +handles this type of table and will return a filtered table with the same structure. + + + + + @Manual{, + title = {R: A Language and Environment for Statistical Computing}, + author = {{R Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2014}, + url = {http://www.R-project.org/}, + } + + + diff -r 000000000000 -r 3362f5b5099f test-data/filtered-0.05.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered-0.05.tab Sun Jun 16 11:27:12 2019 -0400 @@ -0,0 +1,43 @@ +1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 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