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 1.8.2 Index]