plotPathway: Plot DE output on a selected KEGG pathway map

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

Description

Plot DE output on a selected KEGG pathway map

Usage

plotPathway(DEoutput, fdr = 0.05, pathway_IDs = c("05200", "04110"),
  genome = "hg38")

Arguments

DEoutput	A tab-seperated edgeR/DESeq2 output file, using EdgeR_wrapper or DESeq_wrapper
fdr	FDR cutoff for Diff-Exp genes.
pathway_IDs	KEGG ids for the pathways to plot
genome	Select from hg38, mm10, dm6. (although it's agnostic to genome versions in general).

Value

KEGG plot

Examples

deout <- system.file("extdata", "edgeR_output_annotated.tsv", package="vivlib")
plotPathway(DEoutput = deout, fdr = 0.05, pathway_IDs = "05200", genome = "mm10")

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