CreateRdrop: Computes leave-one-out correlations (rDrop) for each CpG

In lissettegomez/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Description

Computes leave-one-out correlations (rDrop) for each CpG

Usage

CreateRdrop(data, method = c("pearson", "spearman"))

Arguments

data	a dataframe with rownames = sample IDs, column names = CpG IDs.
method	method for computing correlation, can be "pearson" or "spearman"

Details

An outlier CpG in a genomic region will typically have low correlation with the rest of the CpGs in a genomic region. On the other hand, in a cluster of co-methylated CpGs, we expect each CpG to have high correlation with the rest of the CpGs. The r.drop statistic is used to identify these co-methylated CpGs here.

Value

A data frame with the following columns:

• CpG : CpG ID

• r_drop : The correlation between each CpG with the sum of the rest of the CpGs

Examples

   data(betaMatrix_ex1)

   CreateRdrop(data = betaMatrix_ex1, method = "pearson")

lissettegomez/coMethDMR documentation built on April 25, 2021, 1:10 p.m.