cor_binary: cor_binary

In zhangjunpeng411/miRSM: Inferring miRNA sponge modules in heterogeneous data

cor_binary

Description

Generation of positively correlated binary matrix between ceRNAs, or ceRNAs and mRNAs

Usage

cor_binary(
  ceRExp,
  mRExp = NULL,
  cor.method = "pearson",
  pos.p.value.cutoff = 0.01
)

Arguments

ceRExp	A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs.
mRExp	NULL (default) or a SummarizedExperiment object. mRNA expression data: rows are samples and columns are mRNAs.
cor.method	The method of calculating correlation selected, including 'pearson' (default), 'kendall', 'spearman'.
pos.p.value.cutoff	The significant p-value cutoff of positive correlation.

Value

A binary matrix.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng-Zhang-2)

References

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008, 9:559.

Examples

data(BRCASampleData)
cor_binary_matrix <- cor_binary(ceRExp, mRExp)

zhangjunpeng411/miRSM documentation built on Sept. 23, 2024, 4:37 a.m.