parse_gctx: Parse GCTX

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.