annot.clusters: Annotate vectors of Illumina probe names, each vector...

Description Usage Arguments Value Examples

Description

Returns a list of matrices with annotations of the CpG sites represented by vector of probe names. Each vector represent a cluster

Usage

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annot.clusters(clusters.list, annot = NULL, annotation.file.name = NULL, required.annotation = c("IlmnID", "Coordinate_37", "UCSC_RefGene_Name", "UCSC_RefGene_Group", "UCSC_CpG_Islands_Name", "Relation_to_UCSC_CpG_Island"))

Arguments

clusters.list

A list in which each element is a vector of illumine probe names.

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.

required.annotation

Names of columns from Illumina annotation file, to be provided as annotation

Value

A list corresponding to clusters.list. Each element in the list is matrix of required.annotations for each of the probes in the vector in the corresponding element in clusters.list.

Examples

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data(betas.7) ## upload methylation data
exposure <- rbinom(ncol(betas.7), 1,prob = 0.5) ## generate random exposure
covariates <- matrix(rnorm(2*ncol(betas.7)), ncol = 2)

data(annot.7)
clusters.list <- assign.to.clusters(betas.7, annot.7)

annotated.clusters <- annot.clusters(clusters.list[1:10], annot = annot.7, required.annotation = c("IlmnID", "Coordinate_37", "UCSC_RefGene_Name", "UCSC_RefGene_Group"))

ftyu1234/Aclust documentation built on May 16, 2019, 3:37 p.m.