generic_scMethrix_function: Function used only for inheritence for Roxygen2...

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

Description

Function used only for inheritence for Roxygen2 documentation. Lists the common function inputs used in the package

Usage

generic_scMethrix_function(
  scm,
  assay,
  new_assay,
  trans,
  verbose,
  n_chunks,
  n_threads,
  h5_dir,
  overlap_type,
  batch_size,
  replace
)

Arguments

scm	scMethrix; the single cell methylation experiment
assay	string; name of an existing assay. Default = "score"
new_assay	string; name for transformed assay. Default = "new_assay"
trans	closure; The transformation function. Default = mean
verbose	boolean; Flag for outputting function status messages. Default = TRUE
n_chunks	integer; Number of chunks to split the scMethrix object in case it is very large. Default = 1
n_threads	integer; Maximum number of parallel instances. Default = 1
h5_dir	string; The directory to use. Will be created if it does not exist. Default = NULL
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.
batch_size	integer; The maximum number of elements to process at once.
replace	boolean; flag for whether to delete the contents of h5_dir before saving

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