mask_by_coverage: Masks CpGs by coverage

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Masks CpGs by coverage

Usage

mask_by_coverage(
  scm = NULL,
  assay = "score",
  low_threshold = NULL,
  avg_threshold = NULL,
  n_threads = 1,
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
assay	string; name of an existing assay. Default = "score"
low_threshold	numeric; The minimal coverage allowed. Everything below will get masked. If NULL, this will be ignored.
avg_threshold	numeric; The max average coverage. Typical value is 2, as there should only be 2 reads per cell. If NULL, this will be ignored.
n_threads	integer; Number of parallel instances. Can only be used if scMethrix is in HDF5 format. Default = 1
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Details

Takes scMethrix object and masks sites with low overall or high average coverage by putting NA for assay values. The sites will remain in the object and all assays will be affected.

low_threshold is used to mask sites with low overall coverage. avg_threshold is used to mask sites with high aberrant counts. For single cell data, this is typically CpG sites with an average count > 2, as there are only two strands in a cell to sequence.

Value

An object of class scMethrix

Examples

data('scMethrix_data')
mask_by_coverage(scMethrix_data,low_threshold=2, avg_threshold=2)

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.