get.feature.probe: get.feature.probe to select probes within promoter regions or...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

get.feature.probe is a function to select the probes falling into distal feature regions or promoter regions.

This function selects the probes on HM450K that either overlap distal biofeatures or TSS promoter.

Usage

get.feature.probe(
  feature = NULL,
  TSS,
  genome = "hg38",
  met.platform = "450K",
  TSS.range = list(upstream = 2000, downstream = 2000),
  promoter = FALSE,
  rm.chr = NULL
)

Arguments

feature	A GRange object containing biofeature coordinate such as enhancer coordinates. If NULL only distal probes (2Kbp away from TSS will be selected) feature option is only usable when promoter option is FALSE.
TSS	A GRange object contains the transcription start sites. When promoter is FALSE, Union.TSS in ELMER.data will be used for default. When promoter is TRUE, UCSC gene TSS will be used as default (see detail). User can specify their own preference TSS annotation.
genome	Which genome build will be used: hg38 (default) or hg19.
met.platform	DNA methyaltion platform to retrieve data from: EPIC or 450K (default)
TSS.range	A list specify how to define promoter regions. Default is upstream =2000bp and downstream=2000bp.
promoter	A logical.If TRUE, function will ouput the promoter probes. If FALSE, function will ouput the distal probes overlaping with features. The default is FALSE.
rm.chr	A vector of chromosome need to be remove from probes such as chrX chrY or chrM

Details

In order to get real distal probes, we use more comprehensive annotated TSS by both GENCODE and UCSC. However, to get probes within promoter regions need more accurate annotated TSS such as UCSC. Therefore, there are different settings for promoter and distal probe selection. But user can specify their own favorable TSS annotation. Then there won't be any difference between promoter and distal probe selection. @return A GRanges object contains the coordinate of probes which locate within promoter regions or distal feature regions such as union enhancer from REMC and FANTOM5. @usage get.feature.probe(feature, TSS, TSS.range = list(upstream = 2000, downstream = 2000), promoter = FALSE, rm.chr = NULL)

Value

A GRange object containing probes that satisfy selecting critiria.

Examples

# get distal enhancer probe
## Not run: 
Probe <- get.feature.probe()

## End(Not run)
# get promoter probes
## Not run: 
Probe <- get.feature.probe(promoter=FALSE)

## End(Not run)
# get distal enhancer probe remove chrX chrY
Probe2 <- get.feature.probe(rm.chr=c("chrX", "chrY"))

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.