calcInteger: calcInteger()

In navinlabcode/copykit: CopyKit

calcInteger()

Description

Calculates the integer copy number profile for each single cell

Usage

calcInteger(
  scCNA,
  assay = c("bincounts", "smoothed_bincounts", "segment_ratios"),
  method = "fixed",
  ploidy_value = NULL,
  name = "integer",
  penalty = 25,
  BPPARAM = bpparam()
)

Arguments

scCNA	The CopyKit object.
assay	String with the name of the assay to pull data from to calculate integers.
method	Method used to scale the ratio values to integer.
ploidy_value	If method of choice is 'fixed' a ploidy value should be provided.
name	String specifying the name to be used to store the result in the reducedDims of the output.
penalty	An integer passed on to scquantum::ploidy.inference() penalty argument
BPPARAM	A BiocParallelParam specifying how the function should be parallelized.

Details

CopyKit support the following methods for calculating integer copy number matrices

• fixed: When method argument is set to 'fixed' copykit extracts the segment means from the scCNA object and multiplies those means by the value provided in the argument ploidy_value.

• scquantum: When the method argument is set to 'scquantum', CopyKit applies ploidy.inference function to perform a sample wise calculation returning the estimated compuational ploidy for every single cell

Value

The CopyKit object with an assay slot named 'integer' that contains a data frame with cells as columns and integerized segments as rows. And, in case of method = 'scquantum' CopyKit adds three new elements to colData named 'ploidy' and 'ploidy_score' and the 'confidence ratio' obtained from scquantum for each cell.

Examples

copykit_obj <- mock_bincounts(ncells_diploid = 0, ncells = 10)
copykit_obj <- calcInteger(copykit_obj, method = "scquantum")

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.