DCGL (version 2.1.2)

rLinkfilter: Filter gene coexpression links according to correlation coefficient value

Description

Keep a fraction of the links (gene pairs) with the higher correlation values than user given threshold (specified with 'cutoff').

Usage

rLinkfilter(exprs.1, exprs.2, cutoff = 0.8, 
	r.method = c("pearson", "spearman")[1])

Arguments

exprs.1

a data frame or matrix for condition A, with rows as variables (genes) and columns as samples.

exprs.2

a data frame or matrix for condition B, with rows as variables (genes) and columns as samples.

cutoff

the threshold of correlation coefficient value. Default is 0.8.

r.method

a character string to indicate which type of correlation coefficient, 'pearson' (default) or 'spearman', will be computed.

Details

Each gene link is associated with two correlation values (one out of condition A and the other out of condition B) and thus a list of 'maximum absolute values' of the two values is decided. Then these links have larger correlation coefficient than threshold are kept.

Examples

data(exprs)
rLinkfilter(exprs[1:100,1:16],exprs[1:100,17:63],cutoff=0.8,r.method='pearson')