Remove loci that are uncovered across all samples

remove_uncovered(scm = NULL, n_threads = 1, verbose = TRUE)

Arguments

scm	`scMethrix`; the single cell methylation experiment
n_threads	integer; Maximum number of parallel instances. Default = 1
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Value

An object of class scMethrix

Details

Takes scMethrix object and removes loci that are uncovered across all samples

Examples

data('scMethrix_data')
# Remove uncovered CpGs after subsetting to a single sample
remove_uncovered(subset_scMethrix(scMethrix_data, samples = "C1", by="include"))
#> Subsetting CpG sites...
#>    Subsetting by samples
#> Subset in 0.07s
#> Removing uncovered CpGs...
#> Removed 105 [36.71%] uncovered loci of 286 sites (0.01s)
#> An object of class scMethrix
#>    n_CpGs: 181
#>    n_samples: 1
#>    assays: score, counts
#>    reduced dims: 
#>    is_h5: FALSE
#>    Reference: hg19
#>    Physical size: 33.9 Kb