parse_gctx: Parse a GCTX file into the workspace as a GCT object
In cmap/cmapR: CMap Tools in R

Description Usage Arguments Details Value See Also Examples

Parse a GCTX file into the workspace as a GCT object

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parse.gctx(...)

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

`...`	arguments passed on to `parse_gctx`
`fname`	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 indicies 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 indicies will be parsed from the file.
`matrix_only`	boolean indicating whether to parse only the matrix (ignoring row and column annotations)

parse_gctx also supports parsing of plain text GCT files, so this function can be used as a general GCT parser.

a GCT object

Other GCTX parsing functions: GCT, append.dim(), fix.datatypes(), process_ids(), read.gctx.ids(), read.gctx.meta(), write.gctx.meta(), write.gctx(), write.gct()

gct_file <- system.file("extdata", "modzs_n25x50.gctx", package="cmapR")
(ds <- parse_gctx(gct_file))

# matrix only
(ds <- parse_gctx(gct_file, matrix_only=TRUE))

# only the first 10 rows and columns
(ds <- parse_gctx(gct_file, rid=1:10, cid=1:10))