gmt2GO: Read a .gmt file and generate a list of gene set sequences.

In miccec/yaGST: Competitive gene set and regulon tests.

Usage

gmt2GO(what)

Arguments

what	either a character string naming a .gmt file or a list of a character string naming .gmt files

Value

a vector of lists (see GO2gmt)

Author(s)

Stefano M. Pagnotta

See Also

GO2gmt, rankedList

Examples

library(yaGST)
data("rankedList")

# create a collection of gene sets
GO <- vector("list", 2)
GO[[1]] <- sample(head(names(rankedList), 5000), 50)
# your reference lik for the gene set
attr(GO[[1]], "link") <- "http://www.enjoy_the_silence.dm" 

GO[[2]] <- sample(head(names(rankedList), 5000), 50)
attr(GO[[2]], "link") <- "http://www.imagine.jl"
names(GO) <- c("geneSet_1", "geneSet_2")
GO

# save the collection 
GO2gmt(GO, "~/my_GO_collection.gtm")
#########
# load a .gmt file
my_GO_collection <- gmt2GO("~/my_GO_collection.gtm")
summary(my_GO_collection)
head(my_GO_collection$geneSet_1)
attr(my_GO_collection[[1]], "link")
attr(my_GO_collection[[1]], "ontology")

miccec/yaGST documentation built on May 23, 2019, 7:35 a.m.