get_region_target_gene {MethReg} | R Documentation

## Obtain target genes of input regions based on distance

### Description

To map an input region to genes there are three options: 1) map region to closest gene tss 2) map region to all genes within a window around the region (default window.size = 500kbp (i.e. +/- 250kbp from start or end of the region)). 3) map region to a fixed number of nearby genes (upstream/downstream)

### Usage

    get_region_target_gene(
      regions.gr,
      genome = c("hg38", "hg19"),
      method = c("genes.promoter.overlap", "window", "nearby.genes", "closest.gene.tss"),
      promoter.upstream.dist.tss = 2000,
      promoter.downstream.dist.tss = 2000,
      window.size = 500 * 10^3,
      num.flanking.genes = 5,
      rm.promoter.regions.from.distal.linking = TRUE
    )

### Arguments

`regions.gr` | A Genomic Ranges object (GRanges) or a SummarizedExperiment object (rowRanges will be used)
`genome` | Human genome of reference "hg38" or "hg19"
`method` | How genes are mapped to regions: region overlapping gene promoter ("genes.promoter.overlap"); or genes within a window around the region ("window"); or a fixed number genes upstream and downstream of the region ("nearby.genes"); or closest gene tss to the region ("closest.gene.tss")
`promoter.upstream.dist.tss` | Number of base pairs (bp) upstream of TSS to consider as promoter regions. Defaults to 2000 bp.
`promoter.downstream.dist.tss` | Number of base pairs (bp) downstream of TSS to consider as promoter regions. Defaults to 2000 bp.
`window.size` | When `method = "window"`, number of base pairs to extend the region (+- window.size/2). Default is 500kbp (or +/- 250kbp, i.e. 250k bp from start or end of the region)
`num.flanking.genes` | When `method = "nearby.genes"`, set the number of flanking genes upstream and downstream to search.Defaults to 5. For example, if num.flanking.genes = 5, it will return the 5 genes upstream and 5 genes downstream of the given region.
`rm.promoter.regions.from.distal.linking` | When performing distal linking with method = "windows", "nearby.genes" or "closest.gene.tss", if set to TRUE (default), probes in promoter regions will be removed from the input.

### Details

For the analysis of probes in promoter regions (promoter analysis), we recommend setting `method = "genes.promoter.overlap"`.

For the analysis of probes in distal regions (distal analysis), we recommend setting either `method = "window"` or `method = "nearby.genes"`.

Note that because `method = "window"` or `method = "nearby.genes"` are mainly used for analyzing distal probes, by default `rm.promoter.regions.from.distal.linking = TRUE` to remove probes in promoter regions.

### Value

A data frame with the following information: regionID, Target symbol, Target ensembl ID

### Examples

    library(GenomicRanges)
    library(dplyr)

    # Create example region
    regions.gr <- data.frame(
           chrom = c("chr22", "chr22", "chr22", "chr22", "chr22"),
           start = c("39377790", "50987294", "19746156", "42470063", "43817258"),
           end   = c("39377930", "50987527", "19746368", "42470223", "43817384"),
           stringsAsFactors = FALSE)  %>%
         makeGRangesFromDataFrame

     # map to closest gene tss
     region.genes.promoter.overlaps <- get_region_target_gene(
                          regions.gr = regions.gr,
                          genome = "hg19",
                          method = "genes.promoter.overlap"
     )

     # map to all gene within region +- 250kbp
     region.window.genes <- get_region_target_gene(
                          regions.gr = regions.gr,
                          genome = "hg19",
                          method = "window",
                          window.size = 500 * 10^3
     )

     # map regions to n upstream and n downstream genes
     region.nearby.genes <- get_region_target_gene(
                          regions.gr = regions.gr,
                          genome = "hg19",
                          method = "nearby.genes",
                          num.flanking.genes = 5
     )

[Package MethReg version 1.4.0 Index]