qLinkfilter: To 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 (qth) are retained, while the coexpression values of other links are set to zero.
Usage
qLinkfilter(exprs.1, exprs.2, qth)
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.
qth
the cutoff of q-value; must be within [0,1].
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
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 (or formally, false discovery rates). Gene links with q-values of coexpression values in either of two conditions higher than the cutoff (qth) are reserved.