EdgeR_wrapper: A Wrapper for EdgeR over featurecounts output

Description Usage Arguments Value Examples

View source: R/DiffExp_wrapper.R

Description

A Wrapper for EdgeR over featurecounts output

Usage

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EdgeR_wrapper(fcountOutput, numReplicates = 4, fdr = 0.01,
  Output = "edger_output.tsv", col_order = 1, heatmap_topN = 20,
  pdfReport = "edger_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

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

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