Subsets methrix object based on given conditions.

Subsets methrix object based on given conditions.

subset_methrix(
  m,
  regions = NULL,
  contigs = NULL,
  samples = NULL,
  overlap_type = "within"
)

Arguments

m

methrix object
regions

genomic regions to subset by. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
contigs

chromosome names to subset by
samples

sample names to subset by
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 foverlaps function of the data.table package.

Value

An object of class methrix

Details

Takes methrix object and filters CpGs based on coverage statistics

Examples

data('methrix_data')
#Subset to chromosome 1
subset_methrix(methrix_data, contigs = 'chr21')

#> -Subsetting by contigs
#> An object of class methrix
#>    n_CpGs: 540
#> n_samples: 4
#>     is_h5: FALSE
#> Reference: hg19