transform_assay: Transforms an assay in an 'scMethrix' object.

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

Description

Transforms an assay in an scMethrix object.

Usage

transform_assay(
  scm,
  assay = "score",
  new_assay = "new_assay",
  trans = NULL,
  h5_temp = NULL
)

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
h5_temp	string; temporary directory to store the temporary HDF5 files

Details

Uses the inputted function to transform an assay in the scMethrix object. The function is applied column-wise as to optimize how HDF5 files access sample data.

If HDF5 objects are used, transform functions need to accept 'DelayedMatrix' (e.g., from DelayedMatrixStats). Otherwise,

Value

An scMethrix object

Examples

data('scMethrix_data')
transform_assay(scMethrix_data,assay="score",new_assay="plus1",trans=function(x){x+1})

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