Read a GMT file into a data frame — read_gmt • clustermole

Read a GMT file into a data frame

Usage

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

Arguments

file: A file path, URL, or connection.
geneset_label: Output column name for gene sets (GMT column 1).
gene_label: Output column name for genes (GMT columns 3 onward).

Value

A data frame with gene sets and genes, one gene per row.

Examples

if (FALSE) { # \dontrun{
gmt <- "http://software.broadinstitute.org/gsea/msigdb/supplemental/scsig.all.v1.0.symbols.gmt"
gmt_tbl <- read_gmt(gmt)
head(gmt_tbl)
} # }