Transforms an assay in an scMethrix object. — transform

Transforms an assay in an scMethrix object.

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

Value

An scMethrix object

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,

Examples

data('scMethrix_data')
transform_assay(scMethrix_data,assay="score",new_assay="plus1",trans=function(x){x+1})
#> An object of class scMethrix
#>    n_CpGs: 286
#>    n_samples: 4
#>    assays: score, counts, plus1
#>    reduced dims: 
#>    is_h5: FALSE
#>    Reference: hg19
#>    Physical size: 56.7 Kb