mapGCT package

mapGCT is a simple package to read and write gct file. It can also be used to add extra row or column descriptors to the existing GCT_object.

Install instructions

Dependencies are listed in DESCRIPTION

Installing from source

The latest version can be installed directly from bitbucket using devtools::install_github("ElucidataInc/mapGCT").

Alternatively, R's install.packages function can be used at a tarball of the mapGCT archive. This archive can be generated by cloning this repository and doing the following:

# make a gzip tar ball of the repo
R CMD build mapGCT
# makes mapGCT_x.x.x.tar.gz

# check that the package is ok
R CMD check mapGCT_x.x.x.tar.gz	

Once tarball is created, execute following command in R terminal:

install.packages("mapGCT_x.x.x.tar.gz", type="source", repos=NULL)
library("mapGCT")

Code Examples

There are four main functions for parsing and writing gct files:

1. to_GCT() Converts the given matrix, column descriptions and row descriptions to a GCT_object
2. write_gct write a GCT_object to disk in gct format
3. parse_gct parse or load a gct file into the workspace as a GCT_object
4. annotate_gct Add row or column annotations to GCT_object. Can be used to add add extra columns to gct_object

Usages

These functions can be called as follows:

# Convert to GCT_object class
ds <- to_GCT(mat = gct_mat, cdesc = col_desc, rdesc = row_desc)

# Write GCT_object to disk
write_gct(ds, "dataset.gct", precision=2)

# Read gct file in R
gct_file <- system.file("extdata", "example_n50x100.gct", package="mapGCT")
ds <- parse_gct(gct_file)

# Add column annotations
ds <- annotate_gct(ds, col_annotate)