breastdata: Breast cancer gene expression + DNA copy number data set from...

In PMA2: Penalized Multivariate Analysis

Breast cancer gene expression + DNA copy number data set from Chin et. al. and used in Witten, et. al. See references below.

Description

This data set consists of gene expression and DNA copy number measurements on a set of 89 samples. The data set can be used to perform integrative analysis of gene expression and DNA copy number data, as in . That is, we can look for sets of genes that are associated with regions of chromosomal gain/loss.

Must be downloaded from https://github.com/Ali-Mahzarnia/PMA2/ and put into the folder PMA/data

Format

The format is a list containing the following elements: - dna: a 2149x89 matrix of CGH spots x Samples - rna: a 19672x89 matrix of Genes x Samples - chrom: a 2149-vector of chromosomal location of each CGH spot - nuc: a 2149-vector of nucleotide position for each CGH spot - gene: a 19672-vector wiith an accession number for each gene - genenames: a 19672-vector with a name for each gene - genechr: a 19672-vector with a chromosomal location for each gene - genedesc: a 19672-vector with a description for each gene - genepos: a 19672-vector with a nucleotide position for each gene

Details

Missing values were imputed using 5-nearest neighbors (see library pamr).

References

Ali Mahzarnia, Alexander Badea (2022), Joint Estimation of Vulnerable Brain Networks and Alzheimer’s Disease Risk Via Novel Extension of Sparse Canonical Correlation at bioRxiv.

Examples

data(breastdata)
attach(breastdata)
PlotCGH(dna[,1], chrom=chrom, main="Sample 1", nuc=nuc)
detach(breastdata)

PMA2 documentation built on May 12, 2022, 9:06 a.m.