myGO_KEGG: GO and KEGG analyse for the DEG

In Lian-Lab/LIANLAB: To integrate analysis methods and simplify analysis process

Description

GO and KEGG analyse for the DEG

Usage

myGO_KEGG(
  species = "m",
  up_gene,
  down_gene,
  png.width = 1000,
  png.height = 500,
  pdf.width = 700,
  pdf.height = 5,
  show = 20,
  filename = NULL
)

Arguments

species	species of genes
up_gene	character of up genes
down_gene	character of down genes
png.width	width of the figure in png
png.height	height of the figure in png
pdf.width	width of the figure in pdf
pdf.height	height of the figure in pdf
show	number of the pathway to show
filename	the name of the generated file

Examples

## Not run: 
input.file <- system.file('extdata','DEG.csv',package = 'LIANLAB')
DEG_matrix <- read.csv(input.file, header = TRUE, row.names = 1)
up_gene <- rownames(subset(DEG_matrix,avg_logFC > 0))
down_gene <- rownames(subset(DEG_matrix,avg_logFC < 0))
DEG <- myGO_KEGG(species="h",up_gene,down_gene)

## End(Not run)

Lian-Lab/LIANLAB documentation built on June 23, 2021, 5:37 a.m.