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

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Description

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

Usage

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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.

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.

Value

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

Author(s)

Bao-Hong Liu, Hui Yu, Jing Yang

Examples

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