kobas.background {KOBAS} R Documentation

Load a gene set collection from a GMT file as a GSEA background model.

Description

Usage

kobas.background(gmt,
    min.size = 0,
    max.size = 2147483647,
    duplicate = "error");

Arguments

gmt

the GMT file path. [as string]

min.size

the minimum number of members of the gene set, gene sets smaller than this value will be removed. Default 0 means no filtering. [as integer]

max.size

the maximum number of members of the gene set, gene sets larger than this value will be removed. Default 2147483647 means no filtering. [as integer]

duplicate

the strategy for the duplicated gene set id in the GMT file, could be error (default, throw an exception) or keep (keep the first one). [as string]

Details

The size property of the returned background model is the union size of all gene set members, it is NOT the number of genes in the expression matrix. The GSEA analysis always uses the number of genes in the ranked list as the population size N.

Authors

gseakit

Value

a Background model.

clr value class

Examples

[Package KOBAS version 1.0.0.0 Index]