data.prep {MVisAGe}

A Function for Preparing mRNAseq and Copy Number Data Matrices

Description

This function prepares mRNAseq and copy number data matrices for use in other mVisAGe functions.

Usage

data.prep(exp.mat, cn.mat, gene.annot, sample.annot = NULL, log.exp = FALSE,
  gene.list = NULL)

Arguments

exp.mat

A matrix of gene-level expression data (rows = genes, columns = samples). Both row names (gene names) and column names (sample IDs) must be given.

cn.mat

A matrix of gene-level DNA copy number data (rows = genes, columns = samples). DNA methylation data can also be used. Both row names (gene names) and column names (Sample IDs) must be given.

gene.annot

A three-column matrix containing gene position information. Column 1 = chromosome number written in the form 'chr1' (note that chrX and chrY should be written chr23 and chr24), Column 2 = position (in base pairs), Column 3 = cytoband.

sample.annot

An optional two-column matrix of sample annotation data. Column 1 = sample IDs, Column 2 = categorical sample annotation (e.g. tumor vs. normal). If NULL, sample annot will be created using the common sample IDs and a single group ('1'). Default = NULL.

log.exp

A logical value indicating whether or not the expression values have been log-transformed. Default = FALSE.

gene.list

Used to restrict the output to a set of genes of interest, e.g. genes identified by GISTIC as having recurrent copy number alterations. Default = NULL, and in this case all genes are used.

Value

Returns a list with four components: cn, exp, gene.annot, and sample.annot. Each of cn, exp, and gene.annot have been restricted to a common set of genes, and these appear in the same order. Similarly, cn, exp, and sample.annot have been restricted to a common set of subjects that appear in the same order.

Examples

exp.mat = tcga.exp.convert(exp.mat)

 cn.mat = tcga.cn.convert(cn.mat)

 data.prep(exp.mat, cn.mat, gene.annot, sample.annot, log.exp = FALSE)