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

In lijingya/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.

Usage

get.feature.probe(feature, TSS, TSS.range = list(upstream = 2000, downstream = 2000), promoter = FALSE, rm.chr = NULL)

Arguments

feature	A GRange object containing biofeature coordinates such as enhancer coordinates. Default is comprehensive genomic enhancer regions from REMC and FANTOM5 which is Union.enhancer data in ELMER.data. 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.
TSS.range	A list specify how to define promoter regions. Default is upstream =2000bp and downstream=2000bp.
promoter	A logical. If it is 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. Once specified, the probes on these chromosome will be removed such as chrX chrY or chrM

Details

TSS: 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.

Value

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.

Author(s)

Lijing Yao (maintainer: [e-mail])

References

Yao L, Shen H, Laird PW, Farnham PJ,Berman BP: Inferring Regulatory Element Landscapes and Transcription Factor Networks from Cancer Methylomes. in revision of Genome Biology

Examples

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

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

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

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.