parse.gctx {cmapR} | R Documentation |
Parse a GCTX file into the workspace as a GCT object
parse.gctx(...) parse_gctx(fname, rid = NULL, cid = NULL, matrix_only = FALSE)
... |
arguments passed on to |
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))