corf: Filter training gene expression features

In aritronath/iMIRAGE: iMIRAGE: imputed miRNA activity from gene expression (Title Case)

Description

Internal function used by imirage.cv, imirage.cv.loop, and imirage.cv to filter informative protein coding genes based on correlation with miRNA expression.

Usage

corf(train_pcg, train_mir, gene_index, num = 50, target = "none")

Arguments

train_pcg	training protein coding expression dataset. a numeric matrix with row names indicating samples, and column names indicating protein coding gene IDs.
train_mir	training miRNA expression dataset. a numeric matrix with row names indicating samples, and column names indicating miRNA IDs
gene_index	either gene name (character) or index (column number) of the miRNA to be imputed.
num	number of informative protein coding genes to be used in constructing imputation model. Default is 50 genes.
target	"none" (default), "ts.pairs", or dataframe/matrix/list. this argument accepts character strings to indicate the use of all candidate genes as predictors ("none), or use built-in TargetScan miRNA-gene pairs ("ts.pairs"). also accepts a dataframe , matrix or list object containing a column with names of miRNA and a column with the names of target genes.

Value

a numeric matrix containing subset of protein coding genes correlated with miRNA of interest.

aritronath/iMIRAGE documentation built on Dec. 29, 2019, 1:28 a.m.