correlateGEandAS {psichomics} | R Documentation

## Correlate gene expression data against alternative splicing quantification

### Description

Test for association between paired samples' gene expression (for any genes of interest) and alternative splicing quantification.

### Usage

    correlateGEandAS(geneExpr, psi, gene, ASevents = NULL, ...)

### Arguments

`geneExpr` | Matrix or data frame: gene expression data
`psi` | Matrix or data frame: alternative splicing quantification data
`gene` | Character: gene symbol for genes of interest
`ASevents` | Character: alternative splicing events to correlate with gene expression of a gene (if `NULL`, the events will be automatically retrieved from the given gene)
`...` | Extra parameters passed to cor.test

### Value

List of correlations where each element contains:

``eventID`` | Alternative splicing event identifier
``cor`` | Correlation between gene expression and alternative splicing quantification of one alternative splicing event
``geneExpr`` | Gene expression for the selected gene
``psi`` | Alternative splicing quantification for the alternative splicing event

### See Also

Other functions to correlate gene expression and alternative splicing: `[.GEandAScorrelation()`

### Examples

    annot <- readFile("ex_splicing_annotation.RDS")
    junctionQuant <- readFile("ex_junctionQuant.RDS")
    psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))

    geneExpr <- readFile("ex_gene_expression.RDS")
    correlateGEandAS(geneExpr, psi, "ALDOA")

[Package psichomics version 1.12.1 Index]