convert_compendium_to_gene_sets: convert_compendium_to_gene_sets

In VCCRI/C3: An R package for cross-species compendium-based cell-type identification for transcriptomic profile

Description

This function converts a marker gene matrix into marker gene gene-sets and gene universe.

Usage

convert_compendium_to_gene_sets(specific.compendium)

Arguments

specific.compendium

A marker gene matrix as returned by 'make_marker_gene_compendium' (i.e., marker.genes.matrix). That is, a matrix containing the presence (1) / absence (0) information for marker genes in each cell type / tissue. Rows denote genes, columns denote individual tissues or cell types.

Details

This function converts a marker gene matrix into marker gene gene-sets and gene universe.

Value

This function returns a list with two sub-list consisting of marker gene gene-sets and the gene universe for each cell type or tissue, with elements of the sub-lists corresponding to columns of the input matrix.

Examples

specific.compendium<-matrix(sample(0:1, 100, replace=T), 10, 10)
rownames(specific.compendium)<-c("ENSG00000100053", "ENSG00000109846", "ENSG00000244752", "ENSG00000138083", "ENSG00000181449", "ENSG00000160202", "ENSG00000007372", "ENSG00000117707", "ENSG00000101144", "ENSG00000277354")
colnames(specific.compendium)<-c("cell1", "cell2", "cell3", "cell4", "cell5", "cell6", "cell7", "cell8", "cell9", "cell10")
convert_compendium_to_gene_sets(specific.compendium)

VCCRI/C3 documentation built on May 14, 2019, 8:41 a.m.