SeqGSEA (version 1.12.0)

geneScore: Calculate gene scores by integrating DE and DS scores

Description

Calculate gene scores by integrating DE and DS scores

Usage

geneScore(DEscore, DSscore = NULL, method = c("linear", "quadratic", "rank"), DEweight = 0.5)

Arguments

DEscore

normalized DE scores.

DSscore

normalized DS scores.

method

one of the integration methods: linear, quadratic, or rank; default: linear.

DEweight

any number between 0 and 1 (included), the weight of differential expression scores (the weight for differential splice is (1-DEweight)).

Value

A vector of gene scores.

Details

The integration methods including "linear", "quadratic", and "rank" are detailed in Wang and Cairns (2013). Here the rank method refers only to the method using data-set-specific ranks.

For DE-only analysis, just specify DEweight to be 1, and the DSscore value can be NULL.

References

Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.

See Also

genePermuteScore

Examples

data(DEscore, package="SeqGSEA")
data(DSscore, package="SeqGSEA")
# linear combination with weight for DE 0.3 
gene.score <- geneScore(DEscore, DSscore, method="linear", DEweight = 0.3)
# DE only analysis 
gene.score <- geneScore(DEscore, DEweight = 1)