sesameData_getProbesByGene: Get Probes by Genes or Gene Promoters

In zwdzwd/sesameData: Supporting Data for SeSAMe Package

Get Probes by Genes or Gene Promoters

Description

Get probes mapped to a gene. All transcripts for the gene are considered. The function takes a gene name as appears in UCSC RefGene database. The platform and reference genome build can be changed with 'platform' and 'genome' options. The function returns a vector of probes that falls into the given gene.

Usage

sesameData_getProbesByGene(
  gene_name = NULL,
  platform = NULL,
  promoter = FALSE,
  upstream = 1500,
  downstream = 1500,
  genome = NULL
)

Arguments

gene_name	gene name, if NULL return all genes
platform	EPIC or HM450
promoter	if TRUE, use TSS instead of the whole gene
upstream	number of bases to expand upstream of target gene
downstream	number of bases to expand downstream of target gene
genome	hg38 or hg19

Value

GRanges containing probes that fall into the given gene

Examples

## download needed data
sesameDataCache(c("Mammal40.address", "genomeInfo.hg38"))

## get all probes overlapping with DNMT3A
probes <- sesameData_getProbesByGene(
    'DNMT3A', "Mammal40", upstream=500, downstream=500)

## get the promoter-associated probes
probes <- sesameData_getProbesByGene('DNMT3A', "Mammal40", promoter = TRUE)

zwdzwd/sesameData documentation built on Feb. 27, 2024, 4:37 p.m.