gctx2h5 {signatureSearch} | R Documentation |
Read matrix-like data from large gctx file in chunks and write result back to an HDF5 file.
gctx2h5(gctx, cid, new_cid = cid, h5file, by_ncol = 5000, overwrite = TRUE)
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' |
HDF5 file
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)