calcRatios: Calculates the ratios from a matrix of counts

In navinlabcode/copykit: CopyKit

Calculates the ratios from a matrix of counts

Description

Calculates the ratios from a matrix of counts

Usage

calcRatios(
  scCNA,
  assay = c("ft", "bincounts", "smoothed_bincounts"),
  fun = c("mean", "median")
)

Arguments

scCNA	The scCNA object
assay	String with the name of the assay to pull data from to calculate the ratios.
fun	A string indicating the summarizing function to be used.

Details

Calculates a sample-wise normalization of the selected assay by the mean bin counts returns ratios where a value of 1 corresponds to the neutral copy number state of the sample

Value

A ratio matrix within the slot assay(scCNA, 'ratios') can be accessed with ratios.

Examples

copykit_obj <- mock_bincounts()
copykit_obj <- calcRatios(copykit_obj)

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