mogsva {GSVA} R Documentation

Run the multi-omics GSVA (moGSVA) analysis on the given multi-omics dataset.

Description

Usage

mogsva(x, geneSet, opts);

Arguments

x

the multi-omics dataset object that is created by the mo_layers function. [as MultiOmicsDataset]

geneSet

the gene set collection, it could be a GSEA Background model, a GMT file path or other data that could be cast into the background model.

opts

the running configuration object that is created by the mogsva_opts function. [as MultiOmicsGsvaOptions]

env

the R# runtime environment. [as Environment]

Details

The scoring of each omics layer is performed independently (the kernel density estimation never mixes the features from the different omics), then the omics specific enrichment scores are fused by the configured weight strategy.

Authors

gseakit

Value

a MultiOmicsGsvaResult object which contains the fused pathway activity matrix, the per-omics scores, the pathway weights, the omics contribution decomposition and the permutation test p-value table (when permutations is greater than zero).

clr value class

Examples

[Package GSVA version 1.0.0.0 Index]