correlateGEandAS: Correlate gene expression data against alternative splicing...

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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")

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.