run_edgeR {systemPipeR} | R Documentation

## Runs edgeR

### Description

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.

### Usage

    run_edgeR(countDF, targets, cmp, independent = TRUE, paired = NULL, mdsplot = "")

### Arguments

`countDF` | `date.frame` containing raw read counts
`targets` | targets `data.frame`
`cmp` | `character matrix` where comparisons are defined in two columns. This matrix should be generated with `readComp()` from the targets file. Values used for comparisons need to match those in the `Factor` column of the targets file.
`independent` | If `independent=TRUE` then the `countDF` will be subsetted for each comparison. This behavior can be useful when working with samples from unrelated studies. For samples from the same or comparable studies, the setting `independent=FALSE` is usually preferred.
`paired` | Defines pairs (`character vector`) for paired analysis. Default is unpaired (`paired=NULL`).
`mdsplot` | Directory where `plotMDS` should be written to. Default setting `mdsplot=""` will omit the plotting step.

### Value

`data.frame` containing `edgeR` results from all comparisons. Comparison labels are appended to column titles for tracking.

### Author(s)

Thomas Girke

### References

Please properly cite the `edgeR` papers when using this function: http://www.bioconductor.org/packages/devel/bioc/html/edgeR.html

### See Also

`run_DESeq2`, `readComp` and `edgeR` vignette

### Examples

    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

[Package systemPipeR version 1.21.6 Index]