parse_gctx {signatureSearch} | R Documentation

## Parse GCTX

### Description

Parse a GCTX file into the R workspace as a GCT object

### Usage

    parse_gctx(
      fname,
      rid = NULL,
      cid = NULL,
      set_annot_rownames = FALSE,
      matrix_only = FALSE
    )

### Arguments

`fname` | character(1), path to the GCTX file on disk
`rid` | either a vector of character or integer row indices or a path to a grp file containing character row indices. Only these indices will be parsed from the file.
`cid` | either a vector of character or integer column indices or a path to a grp file containing character column indices. Only these indices will be parsed from the file.
`set_annot_rownames` | boolean indicating whether to set the rownames on the row/column metadata data.frames. Set this to false if the GCTX file has duplicate row/column ids.
`matrix_only` | boolean indicating whether to parse only the matrix (ignoring row and column annotations)

### Value

gct object

### Examples

    gctx <- system.file("extdata", "test_sample_n2x12328.gctx",
                        package="signatureSearch")
    gct <- parse_gctx(gctx)

[Package signatureSearch version 1.4.6 Index]