calcDistNearestTSS: Calculate distance from region to nearest TSS

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

Description

Idea For a given region R linked to X genes G merge R with nearest TSS for G (multiple) this will increse nb of lines i.e R1 - G1 - TSS1 - DIST1 R1 - G1 - TSS2 - DIST2 To vectorize the code: make a granges from left and onde from right and find distance collapse the results keeping min distance for equals values

Usage

calcDistNearestTSS(links, TRange, tssAnnot)

Arguments

links	Links to calculate the distance
TRange	Genomic coordinates for Tartget region
tssAnnot	TSS annotation

Author(s)

Tiago C. Silva

Examples

## Not run: 
 data <- ELMER:::getdata("elmer.data.example")
  NearbyGenes <- GetNearGenes(data = data, 
                              probes = c("cg15924102", "cg24741609"),  
                              numFlankingGenes = 20)
  NearbyGenes <- ELMER:::calcDistNearestTSS(
       links = NearbyGenes,
       tssAnnot =  getTSS(genome = "hg38"),
       TRange = rowRanges(getMet(data))
       )

## End(Not run)

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