addCorrelation: Correlate miRNA and mRNA expression

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

The function correlates miRNA and mRNA expression from a corObject and fills the cor and pval slots.

Usage

addCorrelation(obj, method = "pearson", subset.miRNA = [e-mail],
  subset.mRNA = [e-mail], common = NULL, alternative = "less", voom = FALSE)

Arguments

obj	a corObject
method	method used for computing correlation: "pearson" or "spearman".
subset.miRNA	Optional, character vector with the names of the miRNAs to correlate. It is recommended that miRNAs are added using addSig function.
subset.mRNA	Optional, character vector with the names of the mRNAs to correlate. It is recommended that mRNAs are added using addSig function.
common	Optional, character vector with the names of the samples to correlate (the samples must appear in both miRNA and mRNA datasets.)
alternative	specification of the alternative hypothesis: "less" (default), "two-sided" or "greater".
voom	If TRUE, normalise NGS data according to voom procedure (check limma package), default is FALSE.

Value

corObject with the slots cor and pval filled.

Note

addCorrelation.R is the slow version of this function, but has the option to compute if there are any influential samples affecting the correlation values.

See Also

corObject-class, cor, addCorrelation.R, addSig

Examples

data(data.obj)

data.obj.correlated<-addCorrelation(data.obj, method="pearson", alternative="less",
 subset.miRNA=c("hsa-let-7e","hsa-miR-122"), subset.mRNA=c("A1BG","A1CF"))

data.obj.correlated@cor
data.obj.correlated@pval

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.