plotWeight: Plot the weights (a.k.a. empirical gene set membership)...

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

Description

This function takes a list of weights (a.k.a. empirical membership), an index (or name) of a specific gene set, then it produces a heatmap (by calling function pheatmap) of these weights.

Usage

plotWeight(weight.list, geneset.index, main="Weight", ...)

Arguments

weight.list	A list of weights (a.k.a. empirical membership) of genes in each gene set. This object is typically obtained from FUNNEL.GSEA.
geneset.index	A specific index or name of the geneset to be plotted.
main	The title of the figure. See pheatmap.
...	Other graphical parameters to be passed to function pheatmap().

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.

See Also

pheatmap

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))
## Generate a heatmap of weights for a particular gene set
    plotWeight(results1$weight.list, "PRIMARY_IMMUNODEFICIENCY")

## End(Not run)

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