ggenrichData: ggenrichData function

In ying-ge/ggEnrich: Visualization of gene set enrichment analysis in publication quality

Description

ggenrichData function is used to preprocess the input file

Usage

ggenrichData(fnames, format, type = "pathways", GENE_MAX = 300, GENE_MIN = 100)

Arguments

fnames	input file or files
format	the way to get the results of the enrichment analysis.(JAVA_GSEA,R_ClusterProfiler,DAVID)
type	analysis type.(pathways,groups_pathway,cluster,groups_cluster) default pathways
GENE_MAX	The maximum number of genes included in GO term,default 300
GENE_MIN	The minimum number of genes included in GO term,default 100

Value

a data set that is used as input to the ggenrichplot,enrichplot_MultiGroup,term_clustering and treeplot functions.

Note

For DAVID format, The first column of the input file submitted by the user is the annotation information(term), the second column is the gene ID(or ENTREZ ID,gene symbol), and the third column is the adj_pval.

ying-ge/ggEnrich documentation built on Nov. 24, 2019, 12:34 p.m.