ReadGMT: ReadGMT
In MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Parse gmt file to a data.frame

write data frame to a gmt file

1
2
3

ReadGMT(gmtpath, limit = c(0, Inf))

writeGMT(gene2path, gmtfile)

`gmtpath`	The path to gmt file.
`limit`	A integer vector of length two, specifying the limit of geneset size.
`gene2path`	A data frame. The columns should be Gene, Pathway ID, and Pathway Name.
`gmtfile`	Path to gmt file.

An data.frame, in which the first column is gene, and the second column is pathway name.

Output gmt file to local folder.

Wubing Zhang

1 2	gene2path = gsGetter(type = "Complex") # writeGMT(gene2path, "Protein_complex.gmt")

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.

MAGeCKFlute index

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

Description