DESeq_wrapper: A Wrapper for DESeq2 over featurecounts output

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

A Wrapper for DESeq2 over featurecounts output

Usage

DESeq_wrapper(fcountOutput, numReplicates = 4, fdr = 0.01,
  Output = "deseq_output.tsv", col_order = 1, heatmap_topN = 20,
  pdfReport = "deseq_report.pdf")

Arguments

fcountOutput	featurecounts output (with control and test columns)
numReplicates	Number of replicates (could be an integer if the number is same for control and test, or a vector with number of replicates for control and for test seperately)
fdr	fdr Cutoff
Output	Output tab seperated file
col_order	How are the columns arranged? (1 = control->test, 2 = test->control)
heatmap_topN	Number of top DE genes to plot in a heatmap (will make rlog trasformed and clustered heatmap) type "all" for all DE genes.
pdfReport	A report of processing

Value

Output file and Pdf Report of DESeq2 analysis

Examples

fc <- system.file("extdata", "fcount_mouse.tsv", package="vivlib")
DESeq_wrapper(fcountOutput = fc,numReplicates = 3, fdr = 0.01,
Output = "deseq_output.tsv", pdfReport = "deseq_report.pdf")

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.