gctx2h5 {signatureSearch} | R Documentation

## 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)

[Package signatureSearch version 1.4.6 Index]