Filter gene coexpression links according to the q-values of expression correlation values

Description

Gene links with q-values of coexpression value pairs in either of two conditions higher than the cutoff are retained, while the coexpression values of other links are set to zero.

Usage

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qLinkfilter(exprs.1, exprs.2, 
	cutoff = 0.25, 
	r.method = c("pearson", "spearman")[1], 
	q.method = c("BH", "holm", "hochberg", "hommel", "bonferroni", "BY", "fdr")[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 cutoff of q-value; must be within [0,1].

r.method

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

q.method

a character string indicating adjust method of p-value, default is 'BH'.

Details

For each of the two conditions, the coexpression values are associated with the corresponding p-values (student T-test of the zero nature of a PCC), and these p-values are sorted and transformed to q-values (false discovery rates). Gene links with q-values of coexpression values in either of two conditions lower than the cutoff are reserved.

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