qLinkfilter: Filter gene coexpression links according to the q-values of...

In DCGL: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

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

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

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

DCGL documentation built on May 1, 2019, 8:38 p.m.