gmt2h5 {signatureSearch} | R Documentation

## 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)

[Package signatureSearch version 1.8.2 Index]