addSig: Select significant miRNAs or mRNAs

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

Description

Select significantly deregulated miRNAs or mRNAs that will be used for correlating their expression.

Usage

addSig(obj, dataset, FC=NA, logratio=foldchange2logratio(FC), slope=NA, pval=NA,
  adj.pval=NA, min.meanExp=NA, up=FALSE, dw=FALSE, manual=NULL) 

Arguments

obj	a corObject with the slots diffexp.miRNA and diffexp.mRNA already defined
dataset	"miRNA" or "mRNA"
FC	minimum FoldChange (in absolute value)
logratio	minimum logratio (in absolute value)
slope	for longitudinal-regression analysis, minimum absolute slope
pval	maximum uncorrected p value.
adj.pval	maximum corrected p value.
min.meanExp	minimum mean expression.
up	Select only upregulated items (TRUE or FALSE).
dw	Select only downregulated items (TRUE or FALSE).
manual	character vector with miRNA or mRNA names.

Value

corObject

The same corObject with the slots sig.miRNA or sig.mRNA including the names of the miRNAs or mRNAs that will be used for correlation.

See Also

corObject-class, addDiffexp, addCorrelation

Examples

data(data.obj)

## select the significant miRNAs and mRNAs
data.obj<-addSig(data.obj, "miRNA", adj.pval=0.05)
data.obj<-addSig(data.obj, "mRNA", adj.pval=0.05, FC=1.5)

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