addDistNearestTSS: Calculate the distance between probe and gene TSS

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

Description

Calculate the distance between probe and gene TSS

Usage

addDistNearestTSS(data, NearGenes, genome, met.platform, cores = 1)

Arguments

data	A multi Assay Experiment with both DNA methylation and gene Expression objects
NearGenes	A list or a data frame with the pairs gene probes
genome	Which genome build will be used: hg38 (default) or hg19.
met.platform	DNA methyaltion platform to retrieve data from: EPIC or 450K (default)
cores	Number fo cores to be used. Deafult: 1

Examples

## Not run: 
 data <- ELMER:::getdata("elmer.data.example")
  NearbyGenes <- GetNearGenes(data = data, 
                              probes = c("cg15924102", "cg24741609"),  
                              numFlankingGenes = 20)
  NearbyGenes <- addDistNearestTSS(data,NearbyGenes)

## End(Not run)

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