Genes_by_pathway_kegg: Genes_by_pathway_kegg

In dengchunyu/scPagwas: A pathway-based polygenic integration method for inferring disease-associated individual cells in single cell sequencing data

Genes_by_pathway_kegg

Description

A few numbers from library(KEGGREST) pathways.list <- keggList("pathway", "hsa") # Pull all genes for each pathway pathway.codes <- sub("path:", "", names(pathways.list)) Genes_by_pathway.kegg <- sapply(pathway.codes,function(pwid){ pw <- keggGet(pwid) if (is.null(pw[[1]]$GENE)) return(NA) pw2 <- pw[[1]]$GENE[c(FALSE,TRUE)] # may need to modify this to c(FALSE, TRUE) for other organisms pw2 <- unlist(lapply(strsplit(pw2, split = ";", fixed = T), function(x)x[1])) return(pw2) })

Usage

data(Genes_by_pathway_kegg)

Format

a list.

Examples

data(Genes_by_pathway_kegg)
str(Genes_by_pathway_kegg)

dengchunyu/scPagwas documentation built on Nov. 29, 2024, 2:53 p.m.