prepareData: This function extracts relevant data for a pair of genes to...

In kkolmus/MolecularAnalyzeR: This package aims at checking correlation between gene expression and copy number variation for cohorts of patients analyzed within The Cancer Genome Atlas project

Description

This function extracts relevant data for a pair of genes to run statistical tests and perform results visualization.

Usage

prepareData(gene1, gene2, CNVdata, normExpData)

Arguments

gene1	gene for which copy number data will be extracted, character string
gene2	gene for which normalized expression data will be extracted, character string
CNVdata	matrix with copy number data, rows are genes, columns are subject IDs
normExpData	matrix with gene counts, rows are genes, columns are subject IDs

Value

data frame with the following columns: 1. patientID 2. copy number data for gene 1 3. normalized expression data for gene 2 4. genotype class of gene 1: amplification/gain, deletion/loss, wild type/WT

Examples

## Not run: prepareData(gene1 = "CDK11A", gene2 = "CFLAR",
                     CNVdata = CNVdata, normExpData = normExpData)
## End(Not run)

kkolmus/MolecularAnalyzeR documentation built on Dec. 21, 2021, 6:46 a.m.