calcDistNearestTSS {ELMER} | R Documentation

## Calculate distance from region to nearest TSS

### 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 <- dplyr::rbind_list(NearbyGenes)
      colnames(NearbyGenes)[1:2] <- c("ID","ensembl_gene_id")
      NearbyGenes <- calcDistNearestTSS(
           links = NearbyGenes,
           tssAnnot =  getTSS(genome = "hg38"),
           TRange = rowRanges(getMet(data))
           )

    ## End(Not run)

[Package ELMER version 2.6.3 Index]