LINCS: LINCS class

In JovingeLabSoftware/ExpSpect: Calculate protein specific biases in gene expression

Description

A class to facilitate working with the level 4 data from the LINCS project. This class does not provide any of the data (which must be obtained under individual agreement with LINCS). However, once obtained, working with their large binary data files will is facilitated by this class.

Usage

lincs = LINCS$new(dataFile, infoFile)
ids <- lincs$getProbes()[1:3]

Arguments

dataFile

path to the level for LINCS data file in hdf5 format (.gctx)

infoFile

path to the instance info data file for the LINCS data file in hdf5 format (.gctx). Note: LINCS provides this data in a tab delimited format (inst.info). However that file is unwieldy to work with in that format as it takes a long time to load and takes a considerable chunk of memory. It is much more efficient to convert it to an hdf5 file with a structure parallel to that of the datafile. This class provides a utility function info2hdf5 that will accomplish this for you. See methods section below.

Format

LINCS class generator

Methods

getProbes()

Returns a vector of HG U133 Plus 2.0 probesets for which data has been imputed from the 978 landmark genes measured directly on the luminex bead arrays by the LINCS

JovingeLabSoftware/ExpSpect documentation built on May 8, 2019, 4:38 p.m.