omics2chrlist {BioMM}R Documentation

Map individual probes into chromosome

Description

Map a set of individual probes from different omics (i.e. SNPs, gene expression probes, CpGs etc.) into the corresponding chromosomes.

Usage

omics2chrlist(data, probeAnno)

Arguments

data

The input dataset (either data.frame or matrix). Rows are the samples, columns are the probes/genes, except that the first column is the label.

probeAnno

The annotation data stored in a data.frame for probe mapping. It must have at least two columns named 'ID' and 'chr'.

Value

A list of matrices with chromosome IDs as the associated list member names. For each matrix, rows are the samples and columns are the probe names, except that the first column is named 'label'.

Examples

 
## Load data from DNA methylation
methylfile <- system.file('extdata', 'methylData.rds', package='BioMM')  
methylData <- readRDS(methylfile)  
## Annotation files for Mapping CpGs into chromosome  
probeAnnoFile <- system.file('extdata', 'cpgAnno.rds', package='BioMM')  
probeAnno <- readRDS(file=probeAnnoFile)  
## Mapping CpGs into Chromosome
dataList <- omics2chrlist(data=methylData, probeAnno)
length(dataList)

[Package BioMM version 1.0.0 Index]