FastKEGG: KEGG analysis via clusterProfiler package

In huangwb8/lucky: Launch Usual Clinical tool for Kind Yield

Description

FastKEGG is a fast way to do KEGG analysis via series funtion of clusterProfiler package and automatically save related files or plots

Usage

FastKEGG(genes, geneList, default.universe = F, organism = "hsa",
  pvalueCutoff = list(enrichKEGG = 0.05, enrichMKEGG = 0.05),
  qvalueCutoff = 0.1, verbose = T, save.path = "KEGG",
  names = "love")

Arguments

genes	a character of gene id.
geneList	a numeric with id names.For example,logFoldChang with ENSEMBL id names.Note that the names of geneList must be the same type of genes
default.universe	whether to use default universe.If default.universe = F,the background genes would be provide by geneList
organism	Species.Default is "hsa"(homo species).
pvalueCutoff	a list of pvalue adjust method for enrichKEGG and enrichMKEGG
qvalueCutoff	cutoff of q value
verbose	LuckyVerbose gseplot running message or not
save.path	the sub path of saved files
names	the main path and part names of saved files

Examples

Plus.library("clusterProfiler")
data(geneList, package='DOSE')
genes <- names(geneList);
genes <- genes[1:2000]
kegg <- FastKEGG(genes = genes,
                organism = 'hsa',
                pvalueCutoff = 0.05,
                qvalueCutoff = 0.2,
                save.path = "KEGG",
                names = "love")
View(kegg)

huangwb8/lucky documentation built on Oct. 16, 2019, 9:01 a.m.