internals: CopyKit internal functions.
In navinlabcode/copykit: CopyKit

CopyKit-internals

R Documentation

CopyKit internal functions.

Description

This document establish setters and getters to facilitate access to fields for the CopyKit class object. The functions provided here are in addition to setters and getters available from the SingleCellExperiment class

Usage

## S4 method for signature 'CopyKit'
segment_ratios(x, withDimnames = TRUE)

## S4 method for signature 'CopyKit'
ratios(x, withDimnames = TRUE)

## S4 method for signature 'CopyKit'
bincounts(x, withDimnames = TRUE)

## S4 method for signature 'CopyKit'
consensus(x, withDimnames = TRUE)

## S4 replacement method for signature 'CopyKit'
consensus(x) <- value

## S4 method for signature 'CopyKit'
phylo(x)

## S4 replacement method for signature 'CopyKit'
phylo(x) <- value

## S4 method for signature 'CopyKit'
consensusPhylo(x)

## S4 replacement method for signature 'CopyKit'
consensusPhylo(x) <- value

## S4 method for signature 'CopyKit'
distMat(x)

## S4 replacement method for signature 'CopyKit'
distMat(x) <- value

## S4 method for signature 'CopyKit'
graph(x)

## S4 replacement method for signature 'CopyKit'
graph(x) <- value

## S4 method for signature 'CopyKit'
show(object)

x %!in% table

ocean_balance_hex

ocean.balance(n)

superclones_pal()

subclones_pal()

find_scaffold_genes(scCNA, genes)

l2e.normal.sd(xs)

overdispersion(v)

parCor(x, BPPARAM = BiocParallel::bpparam())

mergeLevels(
  vecObs,
  vecPred,
  pv.thres = 1e-04,
  ansari.sign = 0.05,
  thresMin = 0.05,
  thresMax = 0.5,
  verbose = 1,
  scale = TRUE
)

combine.func(
  diff,
  vecObs,
  vecPredNow,
  mnNow,
  mn1,
  mn2,
  pv.thres = 1e-04,
  thresAbs = 0
)

Arguments

`x`	CopyKit object.

Format

An object of class character of length 29.

Value

Hexadecimal values for ocean.balance function

The default colors for heatmaps

a named vector of default colors for CopyKit superclones.

a named vector of default colors for CopyKit subclones.

A data frame with the gene HUGO gene symbol and the position on the relevant scaffold from the varbin pipeline.

A numeric vector with least squares sd estimation.

A numerci vector with the estimation of the index of dispersion, which is used when estimating standard errors for each segment mean

A matrix with the pairwise correlation from the segment ratio means.

Getters

segment_ratios:: Returns a data frame of normalized segment ratio means.
ratios:: Returns a data frame of normalized ratio means.
bincounts:: Returns a data frame of binned bincounts.
consensus:: Returns a data frame of normalized segment ratio means for the consensus matrix.
phylo:: Returns a phylo class object with a phylogenetic tree.
consensusPhylo:: Returns a phylo class object with a phylogenetic tree from the consensus matrix.