qpImportNrr: Import non-rejection rates

In rcastelo/qpgraph: Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Import non-rejection rates

Description

Imports non-rejection rates from an external flat file.

Usage

qpImportNrr(filename, nTests)

Arguments

filename	name of the flat file with the data on the non-rejection rates.
nTests	number of tests performed in the estimation of these non-rejection rates.

Details

This function expects a flat file with three tab-separated columns corresponding to, respectively, 0-based index of one of the variables, 0-based index of the other variable, number of non-rejected tests for the pair of variables of that row in the text file. An example of a few lines of that file would be:

6       3       95
6       4       98
6       5       23
7       0       94
7       1       94

After reading the file the function builds a matrix of non-rejection rates by dividing the number of non-rejected tests by nTests. Note that if the flat file to be imported would eventually have directly the rates instead of the number of tests, these can be also imported by setting nTests=1.

This function is thought to be used to read files obtained from the standalone parallel version of qpNrr which can be downloaded from http://functionalgenomics.upf.edu/qp.

Value

A symmetric matrix of non-rejection rates with the diagonal set to the NA value.

Author(s)

R. Castelo and A. Roverato

References

Castelo, R. and Roverato, A. A robust procedure for Gaussian graphical model search from microarray data with p larger than n, J. Mach. Learn. Res., 7:2621-2650, 2006.

See Also

qpNrr

rcastelo/qpgraph documentation built on Oct. 28, 2024, 5:15 a.m.