read_gmt: Read a GMT file into a data frame

In clustermole: Unbiased Single-Cell Transcriptomic Data Cell Type Identification

Read a GMT file into a data frame

Description

Read a GMT file into a data frame

Usage

read_gmt(file, geneset_label = "celltype", gene_label = "gene")

Arguments

file	A connection object or a character string (can be a URL).
geneset_label	Column name for gene sets (first column of the GMT file) in the output data frame.
gene_label	Column name for genes (variable columns of the GMT file) in the output data frame.

Value

A data frame with gene sets as the first column and genes as the second column (one gene per row).

Examples

gmt <- "http://software.broadinstitute.org/gsea/msigdb/supplemental/scsig.all.v1.0.symbols.gmt"
gmt_tbl <- read_gmt(gmt)
head(gmt_tbl)

clustermole documentation built on June 24, 2024, 5:16 p.m.