Description Usage Arguments Details Value See Also Examples
Parse a GCTX file into the workspace as a GCT object
1 2 3 | 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()
1 2 3 4 5 6 7 8 | 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))
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