meta: Auxiliary data objects required by the tutorial

In Haocan223/MetaGSCA: Meta Gene Set Co-expression Analysis

Description

Three objects dedicated for gene sets, sample groupping, and data set names, respectively.

Usage

data(meta)

Format

Three R objects are loaded under the superset name meta.

• genesetsA list of two components, each component comprising gene members of one pathway

• groupsA list of 11 components, each component indicating phenotype labels of one TCGA dataset

• DsetnamesEleven dataset names, e.g., BRCA

Details

genesets includes the gene lists for two signaling pathways. One gene set can be supplied as a primary input to MetaGSCA(), and both gene sets can be supplied altogether as a primary input to MetaGSCA_Multi_Geneset(). groups stores the binary grouping information for all samples of all datasets. The names of 11 components correspond to the dataset names, which coincide to the root names of the dataset RData files. Dsetnames is a character vector of 11 items. It contains the individual dataset names, or the cancer names. Examples include BRCA and KIRP.

Author(s)

Yan Guo, Hui Yu

Examples

data(meta)
sapply(genesets,length)
sapply(groups,table)
Dsetnames

Haocan223/MetaGSCA documentation built on Nov. 19, 2020, 4:34 a.m.