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Simon Larsen SimonLarsen
SimonLarsen
/ parse_geo_series_matrix.r
Last active
January 18, 2022 12:25
R script for reading GEO series matrix file, parsing characteristics and mapping probes to gene IDs
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| library(data.table) | |
| library(foreach) | |
| args <- commandArgs(TRUE) | |
| #### Input files #### | |
| # Series Matrix File | |
| SERIES_FILE <- args[1] | |
| # Platform data table obtained from GEO. | |
| PLATFORM_FILE <- args[2] |
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| library(data.table) | |
| library(org.Hs.eg.db) | |
| extract <- function(D, exp.only=FALSE, tissue=NULL, evidence=c("G","P")) { | |
| if(exp.only) { | |
| D <- D[grepl("exp", D$`evidence type`),] | |
| } | |
| if(!is.null(tissue)) { | |
| keep <- sapply(D[[tissue]], function(x) any(evidence %in% x)) | |
| D <- D[keep,] |