DCGL (version 2.1.2)

percentLinkfilter: Filter gene coexpression links according to the top percent of expression correlation coefficient value

Description

Keep a fraction (specified with 'cutoff') of the links (gene pairs) with the highest max correlation values.

Usage

percentLinkfilter(exprs.1, exprs.2, cutoff = 0.25, 
	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

fraction of links to be retained. Default is 0.25.

r.method

a character string to indicating 'pearson' (default) or 'spearman' correlation coefficient will be computed.

Value

A list with two components of data frames, one for filtered data of condition A, the other for the counterpart of condition B.

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 'maximum absolute values' are sorted in decreasing order. At last, a fraction of gene pairs with the highest max correlation values will be retained.

Examples

data(exprs)
percentLinkfilter(exprs[1:100,1:16],exprs[1:100,17:63],cutoff=0.25,r.method='pearson')