corFinder: Calculate pair-wise correlations between samples using the...

In waldronlab/doppelgangR: Identify likely duplicate samples from genomic or meta-data

Calculate pair-wise correlations between samples using the expr() slots of a list of two ExpressionSets.

Description

This function acts as a wrapper around ComBat (sva package) and cor(), to calculate pairwise correlations within one or between two ExpressionSets.

Usage

corFinder(eset.pair, separator = ":", use.ComBat = TRUE, ...)

Arguments

eset.pair	a list of ExpressionSets, with two elements. If the two elements are identical, return the correlation matrix for pairs of samples in the first element. If not identical, return pairs between the two elements.
separator	Separator between dataset name and sample name. Dataset names are added to sample names to keep track of dataset of origin.
use.ComBat	Use the sva::ComBat function for batch correction of the expr() data between the two datasets.
...	Extra arguments passed to the cor() function.

Value

Returns a matrix of sample-wise Pearson Correlations.

Author(s)

Levi Waldron, Markus Riester, Marcel Ramos

Examples

example("phenoFinder")

corFinder(esets2)

waldronlab/doppelgangR documentation built on Nov. 2, 2024, 11:52 p.m.