geneScore: Calculate gene scores by integrating DE and DS scores
In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description Usage Arguments Details Value Author(s) References See Also Examples

Calculate gene scores by integrating DE and DS scores

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

`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)).

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.

A vector of gene scores.

Xi Wang, xi.wang@newcastle.edu.au

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.

genePermuteScore

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)