one2manySponge: Sparse Partial Correlations On mRNA/miRNA Expression We make...

In Mercedeh66/mirTarRnaSeq: mirTarRnaSeq

Sparse Partial Correlations On mRNA/miRNA Expression We make mirTarRnaSeq compatible to SPONGE package in order to estimate sparse matrix correlation (using elstic net) for prediction potential miRNA-mRNA interaction. Note this function/method is suggested for miRNA/mRNA interactions in many samples with a notable variance of mRNA/miRNA expression. This model also only reports negative sparse partial correlation predictions.

Description

Sparse Partial Correlations On mRNA/miRNA Expression We make mirTarRnaSeq compatible to SPONGE package in order to estimate sparse matrix correlation (using elstic net) for prediction potential miRNA-mRNA interaction. Note this function/method is suggested for miRNA/mRNA interactions in many samples with a notable variance of mRNA/miRNA expression. This model also only reports negative sparse partial correlation predictions.

Usage

one2manySponge(mirna_exp, diff_exp, miranda_sponge_predict, non_null = TRUE)

Arguments

mirna_exp	miRna expression data.frame with miRNA for rows and samples for columns
diff_exp	mRNA expression data.frame with mRNA for rows and samples for columns
miranda_sponge_predict	miRanda sponge compatible matrix produced by miranda_sponge_predict function
non_null	The default for this parameter is TRUE, hence it returns only non-null estimated if FALSE it would return all NULL and TRUE estimates.

Value

matrix adjacency matrix with column names miRNA and row names mRNA

Mercedeh66/mirTarRnaSeq documentation built on April 14, 2023, 6:49 a.m.