gmt2h5: Convert GMT to HDF5 File

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Convert GMT to HDF5 File

Description

Read gene sets from large gmt file in batches, convert the gene sets to 01 matrix and write the result to an HDF5 file.

Usage

gmt2h5(gmtfile, dest_h5, by_nset = 5000, overwrite = FALSE)

Arguments

gmtfile	character(1), path to gmt file containing gene sets
dest_h5	character(1), path of the hdf5 destination file
by_nset	number of gene sets to import in each iteration to limit memory usage
overwrite	TRUE or FALSE, whether to overwrite or to append to existing 'h5file'

Value

HDF5 file

Examples

gmt <- system.file("extdata", "test_gene_sets_n4.gmt", 
        package="signatureSearch")
h5file <- tempfile(fileext=".h5")
gmt2h5(gmtfile=gmt, dest_h5=h5file, overwrite=TRUE)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.