gsGetter: Extract pathway annotation from GMT file.

In MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Description

Extract pathway annotation from GMT file.

Usage

gsGetter(
  gmtpath = NULL,
  type = "All",
  limit = c(0, Inf),
  organism = "hsa",
  update = FALSE
)

Arguments

gmtpath	The path to customized gmt file.
type	Molecular signatures for testing, available datasets include Pathway (KEGG, REACTOME, C2_CP:PID, C2_CP:BIOCARTA), GO (GOBP, GOCC, GOMF), MSIGDB (C1, C2 (C2_CP (C2_CP:PID, C2_CP:BIOCARTA), C2_CGP), C3 (C3_MIR, C3_TFT), C4 (C4_CGN, C4_CM), C5 (C5_BP, C5_CC, C5_MF), C6, C7, H) and Complex (CORUM). Any combination of them are also accessible (e.g. 'GOBP+GOMF+KEGG+REACTOME').
limit	A two-length vector, specifying the minimal and maximal size of gene sets to load.
organism	'hsa' or 'mmu'.
update	Boolean, indicating whether update the gene sets from source database.

Value

A three-column data frame.

Author(s)

Wubing Zhang

Examples

gene2path = gsGetter(type = "REACTOME+KEGG")
head(gene2path)

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.