Extract and summarize methylation or coverage info by regions of interest

get_region_summary(
  m,
  regions = NULL,
  type = "M",
  how = "mean",
  overlap_type = "within",
  na_rm = TRUE,
  elementMetadata.col = NULL,
  verbose = TRUE,
  n_chunks = 1,
  n_cores = 1
)

Arguments

m	`methrix` object
regions	genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a `GenomicRanges` object
type	matrix which needs to be summarized. Coule be `M`, `C`. Default 'M'
how	mathematical function by which regions should be summarized. Can be one of the following: mean, sum, max, min. Default 'mean'
overlap_type	defines the type of the overlap of the CpG sites with the target region. Default value is `within`. For detailed description, see the `findOverlaps` function of the `IRanges` package.
na_rm	Remove NA's? Default `TRUE`
elementMetadata.col	columns in `methrix`@elementMetadata which needs to be summarised. Default = NULL.
verbose	Default TRUE
n_chunks	Number of chunks to split the `methrix` object in case it is very large. Default = 1.
n_cores	Number of parallel instances. `n_cores` should be less than or equal to `n_chunks`. If `n_chunks` is not specified, then `n_chunks` is initialized to be equal to `n_cores`. Default = 1.

Value

a coverage or methylation matrix

Details

Takes methrix object and summarizes regions

Examples

data('methrix_data')
get_region_summary(m = methrix_data,
regions = data.table(chr = 'chr21', start = 27867971, end =  27868103),
type = 'M', how = 'mean')
#> -Checking for overlaps..
#> -Summarizing by average
#> -Done! Finished in:0.100s elapsed (0.120s cpu)
#>      chr    start      end n_overlap_CpGs rid        C1        C2   N1
#> 1: chr21 27867971 27868103              4   1 0.4055556 0.2378247 0.95
#>           N2
#> 1: 0.9058442