run_edgeR {systemPipeR} | R Documentation |
Convenience wrapper function to identify differentially expressed genes
(DEGs) in batch mode with the edgeR
GML method for any number of pairwise
sample comparisons specified under the cmp
argument. Users are strongly
encouraged to consult the edgeR
vignette for more detailed information
on this topic and how to properly run edgeR
on data sets with more
complex experimental designs.
run_edgeR(countDF, targets, cmp, independent = TRUE, paired = NULL, mdsplot = "")
countDF |
|
targets |
targets |
cmp |
|
independent |
If |
paired |
Defines pairs ( |
mdsplot |
Directory where |
data.frame
containing edgeR
results from all comparisons. Comparison labels are appended to column titles for tracking.
Thomas Girke
Please properly cite the edgeR
papers when using this function:
http://www.bioconductor.org/packages/devel/bioc/html/edgeR.html
run_DESeq2
, readComp
and edgeR
vignette
targetspath <- system.file("extdata", "targets.txt", package="systemPipeR") targets <- read.delim(targetspath, comment="#") cmp <- readComp(file=targetspath, format="matrix", delim="-") countfile <- system.file("extdata", "countDFeByg.xls", package="systemPipeR") countDF <- read.delim(countfile, row.names=1) edgeDF <- run_edgeR(countDF=countDF, targets=targets, cmp=cmp[[1]], independent=FALSE, mdsplot="") pval <- edgeDF[, grep("_FDR$", colnames(edgeDF)), drop=FALSE] fold <- edgeDF[, grep("_logFC$", colnames(edgeDF)), drop=FALSE] DEG_list <- filterDEGs(degDF=edgeDF, filter=c(Fold=2, FDR=10)) names(DEG_list) DEG_list$Summary