order.betas.by.chrom.location: Organizes a matrix of methylation values to be ordered by...

In PeteHaitch/Aclust: Clustering functions and analysis pipeline for methylation outcome data based on clustering and GEEs

Description

The matrix produces lists of ordered methylation matrices, according to location

Usage

order.betas.by.chrom.location(betas, annot = NULL, annotation.file.name = NULL, return.chroms = NULL)

Arguments

betas	An (m by n) matrix of methylation values measured on $n$ participants in $m$ sites.
annot	A preloaded data.table of annotation
annotation.file.name	If annot it not given, annotation.file.name can be provide the file name of the illumine annotation file and the function will load it and convert it to a data.table. If neither annot or annotation.file.name are provided, annotation will be loaded from a Tim Triche's bioconductor R package.
return.chroms	Optional list of chromosomes, if one is interested in specific chromosomes.

Details

Annotation: the package is adjusted to the Illumina annotation (i.e. through part of its column names) but could be easily adjusted to a an attestation data table with different column names.

Value

sites.locations.by.chrom

A list ordered by chromosome number. Each item in this list contains a matrix specifying chromosomal locations of each of the sites in the subsets of sites from betas from the corresponding chromosome. The rows are organized according to chromosomal location.

Examples

data(betas.7) ## upload methylation data
data(annot)
dat.7.ord <- order.betas.by.chrom.location(betas.7, annot = annot)

dat.7.ord$betas.by.chrom$"7"[1:5,1:5]
dat.7.ord$sites.locations.by.chrom$"7"[1:5]

PeteHaitch/Aclust documentation built on May 8, 2019, 1:29 a.m.