sesameData_annoProbes: Annotate Probes by Probe ID

In zwdzwd/sesameData: Supporting Data for SeSAMe Package

Annotate Probes by Probe ID

Description

Columns in the manifests will be added to the annotation. Please note that if unfound, the annotation will be NA. The probe will always be kept in the output.

Usage

sesameData_annoProbes(
  Probe_IDs,
  regs = NULL,
  collapse = TRUE,
  chooseOne = FALSE,
  column = NULL,
  sep = ",",
  return_ov_probes = FALSE,
  return_ov_features = FALSE,
  out_name = NULL,
  platform = NULL,
  genome = NULL,
  silent = FALSE
)

Arguments

Probe_IDs	a character vector of probe IDs
regs	a GenomicRanges::GRanges object against which probes will be annotated, default to genes if not given
collapse	whether to collapse multiple regs into one
chooseOne	choose an arbitrary annotation if multiple exist default to FALSE. which concatenates all with ","
column	which column in regs to annotate, if not given return all overlapping probes
sep	the delimiter for collapsing
return_ov_probes	if TRUE will return overlapping probes in a GRanges object.
return_ov_features	if TRUE will return overlapping features in a GRanges object.
out_name	column header of the annotation, use column if not given
platform	EPIC, MM285 etc. will infer from Probe_IDs if not given
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.
silent	suppress messages

Value

a GRanges with annotated column If a probe has no overlap with regs, it will be included in the results with NA. But if a probe is not included in the manifest (due to mappability), it won't be included in the results.

Examples

library(GenomicRanges)
sesameDataCache(c(
    "genomeInfo.mm10", "MM285.address",
    "genomeInfo.hg38", "Mammal40.address"))

regs = sesameData_getTxnGRanges("mm10")
Probe_IDs = names(sesameData_getManifestGRanges("MM285"))
anno = sesameData_annoProbes(Probe_IDs, promoters(regs), column="gene_name")

## get all genes associated with a probe set
genes = sesameData_getTxnGRanges("hg38", merge2gene = TRUE)
anno = sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, return_ov_features=TRUE)

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