weightPerGene: Get weights (a.k.a. empirical gene set membership) of a list...

In Thakar-Lab/FUNNEL-GSEA-R-Package: FUNNEL-GSEA: FUNctioNal ELastic-net Regression in time-course Gene Set Enrichment Analysis

Description

This is a convenience function that extracts weights (a.k.a. empirical gene set membership) of a vector of genes of interest from a weight list, which is typically computed by FUNNEL.GSEA().

Usage

weightPerGene(weight.list, genesOfInterest)

Arguments

weight.list	A list of weights (a.k.a. empirical gene set membership) computed from the elastic-net regression.
genesOfInterest	A vector of genes of interest.

Value

A list of weights for the pre-specified genes.

Author(s)

Yun Zhang, Juilee Thakar, Xing Qiu

References

Yun Zhang, Juilee Thakar, Xing Qiu (2016) FUNNEL-GSEA: FUNctioNal ELastic-net Regression in time-course Gene Set Enrichment Analysis, submitted to Bioinformatics.

Examples

## Load the sample data
data("H3N2-Subj1")

## It takes about 10 minutes to run on my Laptop; YMMV.
## Not run: t1 <- system.time(results1 <- FUNNEL.GSEA(X, tt, genesets=genesets))
    weightPerGene(results1$weight.list, c("TLR5", "C3AR1"))

## End(Not run)

Thakar-Lab/FUNNEL-GSEA-R-Package documentation built on May 8, 2019, 9:57 p.m.