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]