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)
`...` | Arguments passed on to `stats:::cor.test.default` alternative indicates the alternative hypothesis and must be one of `"two.sided"`, `"greater"` or `"less"`. You can specify just the initial letter. `"greater"` corresponds to positive association, `"less"` to negative association. method a character string indicating which correlation coefficient is to be used for the test. One of `"pearson"`, `"kendall"`, or `"spearman"`, can be abbreviated. exact a logical indicating whether an exact p-value should be computed. Used for Kendall's tau and Spearman's rho. See ‘Details’ for the meaning of `NULL` (the default). conf.level confidence level for the returned confidence interval. Currently only used for the Pearson product moment correlation coefficient if there are at least 4 complete pairs of observations. continuity logical: if true, a continuity correction is used for Kendall's tau and Spearman's rho when not computed exactly.

### 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

### 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 1.10.2 Index]