Estimate descriptive statistics for each sample

get_stats(
  scm = NULL,
  assay = "score",
  per_chr = TRUE,
  verbose = TRUE,
  ignore_chr = NULL,
  ignore_samples = NULL
)

Arguments

scm	`scMethrix`; the single cell methylation experiment
assay	string; name of an existing assay. Default = "score"
per_chr	boolean; Estimate stats per chromosome. Default TRUE
verbose	boolean; Flag for outputting function status messages. Default = TRUE
ignore_chr	string; list of chromosomes to ignore
ignore_samples	string; list of samples to ignore

Value

data.table of summary stats

Details

Calculate descriptive statistics (mean, median, SD) either by sample or per_chr

Examples

data('scMethrix_data')

#Get stats for each sample and chromosome
get_stats(scMethrix_data)
#> Getting descriptive statistics...
#> Finished in 0.83s
#>     Chr Sample_Name mean_meth median_meth   sd_meth
#> 1: chr1          C1 0.6881720           1 0.4657508
#> 2: chr1          C2 0.7250000           1 0.4493314
#> 3: chr1          C3 0.7277228           1 0.4445489
#> 4: chr1          C4 0.7473684           1 0.4306952
#> 5: chr2          C1 0.6761364           1 0.4613808
#> 6: chr2          C2 0.7108434           1 0.4493931
#> 7: chr2          C3 0.6453488           1 0.4781476
#> 8: chr2          C4 0.5416667           1 0.4982399

#Get stats for each sample
get_stats(scMethrix_data,per_chr = FALSE)
#> Getting descriptive statistics...
#> Finished in 0.83s
#>    Sample_Name mean_meth median_meth   sd_meth
#> 1:          C1 0.6823204           1 0.4623817
#> 2:          C2 0.7177914           1 0.4480300
#> 3:          C3 0.6898396           1 0.4608938
#> 4:          C4 0.6508380           1 0.4736149