extract_genes_by_pathway: Extract DEGs from pathways

In jiangyuan2li/quickpath: Quick Pathway Analysis

Description

Extract DEGs from pathways

Usage

extract_genes_by_pathway(
  pathway,
  deg,
  class = c("mmu", "hsa", "gga"),
  out.name = NULL
)

Arguments

pathway	A vector contains interested pathwat names
deg	A dataframe contains DEGS information
class	Specify which type of gene
out.name	A file name ends with ".xlsx", if specified, the output will be written into this file

Value

A list of DEGS for each pathway

Examples

pathway <- c("Purine metabolism", "PI3K-Akt signaling pathway", "AMPK signaling pathway", "Choline metabolism in cancer")
deg = grab_deg_from_cuffdiff(gene_exp.diff)
deg.list = extract_genes_by_pathway(pathway, deg, class = "mmu")

jiangyuan2li/quickpath documentation built on Dec. 8, 2019, 4:05 p.m.