gene_cpg_finder: gene_cpg_finder

In ND91/ndlib: A list of handy functions

Description

Find the probes associated to a given gene symbol (UCSC) using Regex

Usage

gene_cpg_finder(gene_symbol, annotation.gr)

Arguments

gene_symbol	A (list of) UCSC gene symbol(s)
annotation.gr	GenomicRanges object containing the annotation/features of the GMset (obtained through minfi::getAnnotation())

Value

A (list of) GenomicRanges object(s) containing the CpG annotations associated to the gene of interest

Author(s)

Andrew Y.F. Li Yim

Examples

#Load data
require(minfiData)
baseDir <- system.file("extdata", package = "minfiData")
targets <- read.450k.sheet(base = baseDir)
RGset <- read.450k.exp(targets = targets, recursive = T)
Mset <- preprocessIllumina(rgSet = RGset, bg.correct = T, normalize = "controls", reference = 2)
Rset <- ratioConvert(Mset)
GMset <- mapToGenome(Rset)

annotation.gr <- makeGRangesFromDataFrame(getAnnotation(GMset), keep.extra.columns = T, start.field = "pos", end.field = "pos")

gene_cpg_finder(gene_symbol = "TNF", annotation.gr = annotation.gr)

ND91/ndlib documentation built on Aug. 10, 2020, 11:59 a.m.