gsGetter: Extract pathway annotation from GMT file.

View source: R/gsGetter.R View source: R/.ipynb_checkpoints/gsGetter-checkpoint.R

gsGetterR Documentation

Extract pathway annotation from GMT file.

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)


WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.