Mercurial > repos > iuc > raceid_main
view scripts/raceID_filter.R @ 0:e01c989c7543 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author | iuc |
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date | Sat, 03 Mar 2018 17:34:16 -0500 |
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#!/usr/bin/env Rscript args = commandArgs(trailingOnly=T) script_dir = args[1] config_file = args[2] # Load libs, common functions, source RaceID and Galaxy Params source(paste(script_dir, "common.R", sep="/")) # Read input data x <- read.csv(count_matrix, sep="\t", header=TRUE) rownames(x) <- x[,1] message("Count matrix with %.0f cells and %.0f genes", dim(x)[1], dim(x)[2]) # Control gene filtering # (if blank do nothing) if (!( (!exists("control_genes_filter")) || control_genes_filter == "" || control_genes_filter == "None")){ c_genes <- unlist(strsplit(control_genes_filter, "\\s*,\\s")) for (cg in c_genes){ x <- x[grep(cg, rownames(x), invert=T), -1] message("Filtering against %s yielded %.0f cells and %.0f genes", cg, dim(x)[1], dim(x)[2]) } } else { x <- x[grep("INVALID", rownames(x), invert=T), -1] } if (!filtering){ # No filtering, just return an SCseq object sc <- SCseq(x) saveRDS(sc, output_rdat) quit(status=0) } sc <- SCseq(x) if (c_maxexpr == 0){ c_maxexpr = Inf } # Perform actual filtering beyond this point message("Applying filtering parameters: mintotal = %.0f, minexpr = %.0f, minnumber= %.0f, maxexpr= %.0f, downsample= %.0f, dsn= %.0f, rseed=%.0f", c_mintotal, c_minexpr, c_minnumber, c_maxexpr, c_downsample, c_dsn, c_rseed) sc <- filterdata(sc, mintotal=c_mintotal, minexpr=c_minexpr, minnumber=c_minnumber, maxexpr=c_maxexpr, downsample = c_downsample, dsn=c_dsn, rseed=c_rseed) message("Output matrix yielded %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2]) # Output table write.table(sc@fdata, output_table, row.names = T, col.names = T, sep="\t", quote=F) # Output R object saveRDS(sc, output_rdat)