annot.probe.vec: Annotate vector of Illumina probe names

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

Description

Returns a matrix with annotations of the CpG sites represented by a given vector of probe names

Usage

annot.probe.vec(probe.vec, annot = NULL, annotation.file.name = NULL, required.annotation = c("IlmnID", "Coordinate_36", "Gene_Name", "UCSC_RefGene_Group", "UCSC_CpG_Islands_Name", "Relation_to_UCSC_CpG_Island"))

Arguments

probe.vec	A vector of Illumina 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 matrix of requred.annotations for each of the probes in probe.vec

Examples

data(betas.7)
data(annot)
annot.sites <- annot.probe.vec(rownames(betas.7)[1:10], annot = annot)

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