geneScore {SeqGSEA} | R Documentation

## 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)).

### 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.

### Value

A vector of gene scores.

### Author(s)

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

### 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)

[Package SeqGSEA version 1.20.0 Index]