spia_wrapper: A wrapper over SPIA pathway perturbation analysis for mouse...

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

Description

A wrapper over SPIA pathway perturbation analysis for mouse and human

Usage

spia_wrapper(DEoutput, organism = "mmu", padjCutoff = 0.05, outFile,
  outPlot = NULL)

Arguments

DEoutput	A tab-seperated edgeR/DESeq2 output file, using EdgeR_wrapper or DESeq_wrapper
organism	select from "mmu" (mouse) or "hsa" (human)
padjCutoff	FDR cutoff for the genes to include in the list
outFile	output file to write affected pathways
outPlot	output SPIA two-way evidence plot + output summary (pdf)

Value

a txt file and a pdf file

Examples

## Not run: 
deout <- system.file("extdata", "edgeR_output_annotated.tsv", package="vivlib")
spia_wrapper <- function(DEoutput = deout, organism = "mmu", outFile = "edgeR_spia.txt")

## End(Not run)

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