sesameData_getProbesByRegion: Get probes by genomic region

In zwdzwd/sesameData: Supporting Data for SeSAMe Package

Get probes by genomic region

Description

The function takes a genomic coordinate and output the a vector of probes on the specified platform that falls in the given genomic region.

Usage

sesameData_getProbesByRegion(
  regs,
  chrm = NULL,
  beg = 1,
  end = -1,
  platform = NULL,
  chrm_to_exclude = NULL,
  genome = NULL
)

Arguments

regs	GRanges
chrm	chromosome, when given regs are ignored
beg	begin, 1 if omitted
end	end, chromosome end if omitted
platform	EPICv2, EPIC, HM450, ...
chrm_to_exclude	chromosome to exclude.
genome	hg38, mm10, ... will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.

Value

GRanges of selected probes

Examples

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

## get probes in a region
library(GenomicRanges)
probes = sesameData_getProbesByRegion(
    GRanges('chr5', IRanges(135313937, 135419936)), platform = 'Mammal40')

## get all probes on chromosome 5
probes = sesameData_getProbesByRegion(chrm = "chr5", platform = "Mammal40")

## get all probes on chromosome X
probes = sesameData_getProbesByRegion(chrm = 'chrX', platform = "Mammal40")

## get all probes on both chromosome X and Y
probes = sesameData_getProbesByRegion(
    chrm = c('chrX', 'chrY'), platform = "Mammal40")

## get all autosomal probes
probes = sesameData_getProbesByRegion(
    chrm_to_exclude = c("chrX", "chrY"), platform = "Mammal40")

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