Create a Region Map Between CpGs and Gene Regions

This function generates a map that assigns CpG sites to gene regions, establishing a linkage based on their genomic coordinates and providing a foundation for subsequent region-specific analyses.

Usage

create_region_map(cpg_gr, genes_gr, verbose = FALSE)

Arguments

cpg_gr

A GRanges object containing the genomic positions of CpG sites.

genes_gr

A GRanges object containing the genomic positions of gene regions (e.g., promoters) of interest.

verbose

Boolean; print output statements

Value

A data.frame with mappings between gene IDs and CpG IDs, facilitating associating CpG sites with their corresponding gene regions for downstream analyses.

Examples

library(GenomicRanges)
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> 
#> Attaching package: 'IRanges'
#> The following object is masked from 'package:grDevices':
#> 
#>     windows
#> Loading required package: GenomeInfoDb

# Creating dummy GRanges objects for CpG sites and gene regions
cpg_gr <- GRanges(seqnames=c("chr1", "chr1", "chr2"),
                    ranges=IRanges(start=c(100, 200, 150),
                    end=c(100, 200, 150)))
genes_gr <- GRanges(seqnames=c("chr1", "chr2", "chr2"),
                    ranges=IRanges(start=c(50, 100, 130),
                    end=c(150, 180, 160)))
# Creating a region map using the function
region_map <- create_region_map(cpg_gr, genes_gr)
#> Warning: 'cpg_gr' does not have names, assigning default names.
#> Warning: 'genes_gr' does not have names, assigning default names.