filterCounts: Filter a count table using a table of DE from wrapperDeseq2

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Filter a count table using a table of DE from wrapperDeseq2

Description

This function generates counts, FPKM and TPM tables including only the differentially expressed genes present in the set of DE generated with wrapperDeseq2.

Usage

filterCounts(data.folder, type = c("gene", "isoform", "mirna"))

Arguments

data.folder	a character string indicating the paths of rnaseqCounts/mirnaCounts output folders
type	character with three options: gene, isoform, mirna.

Value

Returns counts, fpkm, tpm data frames for gene and isoforms in countsDE.txt, log2fpkmDE.txt and in log2TPMDE.txt

Author(s)

Raffaele Calogero

Examples

## Not run: 
    system("wget 130.192.119.59/public/test.analysis.zip")
    unzip("test.analysis.zip")
    setwd("test.analysis")
    library(docker4seq)
    wrapperDeseq2(output.folder=getwd(), group="docker", experiment.table="_counts.txt", log2fc=1,
    fdr=0.1, ref.covar="Cov.1", type="gene", batch=FALSE))

    filterCounts(data.folder=getwd(), type="gene")


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.