dri.smooth.cghdata {DRI}R Documentation

Smooth DNA copy number data over a specific window size

Description

A moving average is calculated by chromosomal location of copy number probes using a specified window size.

Usage

dri.smooth.cghdata(DNA.data, Chr, mw = 5)

Arguments

DNA.data matrix of DNA copy number data (rows ordered by genome position
Chr vector of chromosomes on which copy number probes are located (ordered by probes' genome position
mw window size to take moving average over

Details

This function performs one pre-processing method for smoothing copy number data before performing further DNA/RNA integrative analyses. To help eliminate missing values, and reduce noise, for each sample a moving average is taken over a user-specified window size along each chromosome.

Value

DNA.smoothed matrix of DNA copy number data smoothed by a moving average window

Author(s)

Keyan Salari, Robert Tibshirani, and Jonathan R. Pollack

References

Salari, K., Tibshirani, R., and Pollack, J.R. (2009) DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. http://pollacklab.stanford.edu/

See Also

drcorrelate, drcorrelate.null, drsam, drsam.null, dri.fdrCutoff, dri.sig_genes, dri.heatmap, dri.merge.CNbyRNA, dri.smooth.cghdata, runFusedLasso

Examples

data(mySampleData)
attach(mySampleData)

DRI.DNA.processed <- dri.smooth.cghdata(DNA.data, Chr, 5)

[Package DRI version 1.1 Index]