gctx2h5: Convert GCTX to HDF5 File

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

Convert GCTX to HDF5 File

Description

Read matrix-like data from large gctx file in chunks and write result back to an HDF5 file.

Usage

gctx2h5(gctx, cid, new_cid = cid, h5file, by_ncol = 5000, overwrite = TRUE)

Arguments

gctx	character(1), path to gctx file from LINCS
cid	character or integer vector referencing the columns of the matrix to include
new_cid	character vector of the same length as cid, assigning new column names to matrix
h5file	character(1), path of the hdf5 destination file
by_ncol	number of columns 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

gctx <- system.file("extdata", "test_sample_n2x12328.gctx", 
        package="signatureSearch")
h5file <- tempfile(fileext=".h5")
gctx2h5(gctx, cid=1:2, 
        new_cid=c('sirolimus__MCF7__trt_cp', 'vorinostat__SKB__trt_cp'), 
        h5file=h5file, overwrite=TRUE)

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