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

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

`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.

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

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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 Jan. 26, 2021, 9:05 a.m.

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