CpG enrichment from GRanges of reads (MEDIPS-style)

Compute CpG enrichment metrics (relH and GoGe) from a GenomicRanges::GRanges of read spans, using the specified BSgenome. Useful when reads are already represented as genomic ranges rather than extracted directly from a BAM file.

calculateCGEnrichmentGRanges(
  readGRanges = NULL,
  BSgenome = NULL,
  chr.select = NULL
)

Arguments

readGRanges

GRanges Genomic ranges representing fragments (each range = one fragment). Default: NULL (must be supplied).

BSgenome

character(1) Name of a BSgenome package, e.g. "BSgenome.Hsapiens.NCBI.GRCh38". The package must be installed and loadable. Default: NULL.

chr.select

character() or NULL Vector of chromosomes to restrict motif calculation. Default: NULL (use all chromosomes).

Value

A tibble with one row and the following columns:

• relH — sample relH normalised by genome relH.

• GoGe — sample GoGe normalised by genome GoGe.

• nReads — total reads (fragments).

• nReadsWithoutPattern — reads lacking "CG" motif.

• n100bpReads — reads with length >= 100 bp.

• n100bpReadsWithoutPattern — reads >= 100 bp lacking "CG".

Details

relH and GoGe are computed by counting "CG" dinucleotides in the provided fragments and normalising by genome-wide expectations (from calculateGenomicCGDistribution()). Unlike calculateCGEnrichment(), this function assumes reads are already summarised as genomic ranges.

See also

calculateCGEnrichment(), calculateGenomicCGDistribution(), GenomicRanges, BSgenome

Examples

# Runnable toy example with synthetic reads over chr1 (requires a BSgenome)
if (requireNamespace("BSgenome.Hsapiens.NCBI.GRCh38", quietly = TRUE)) {
    n <- 200
    gr <- GenomicRanges::GRanges(
        seqnames = rep(1, n),
        ranges = IRanges::IRanges(
            start = sample(1e6:2e6, n),
            width = sample(80:180, n, replace = TRUE)
        ),
        strand = "*"
    )
    calculateCGEnrichmentGRanges(
        readGRanges = gr,
        BSgenome    = "BSgenome.Hsapiens.NCBI.GRCh38",
        chr.select  = 1
    )
}
#> 
#> Attaching package: ‘BSgenome.Hsapiens.NCBI.GRCh38’
#> The following object is masked from ‘package:BSgenome.Hsapiens.UCSC.hg19’:
#> 
#>     Hsapiens
#> # A tibble: 1 × 6
#>    relH  GoGe nReads nReadsWithoutPattern n100bpReads n100bpReadsWithoutPattern
#>   <dbl> <dbl>  <int>                <int>       <int>                     <int>
#> 1  3.94  1.88    200                   12         161                         9