make.CCFs.tree.consistant: Function to correct CCFs when sum of daughter CCFs > parent...

In amf71/cloneMap: A Package to Construct Visual Representations of the Spatial Distribution of Somatic Clones in a Tissue / Sample

Function to correct CCFs when sum of daughter CCFs > parent CCF

Description

Function to correct CCFs when sum of daughter CCFs > parent CCF

Usage

make.CCFs.tree.consistant(
  tree.mat,
  CCF.data,
  warning.limit = 1,
  parent.adjust = 1,
  decrease.daughters = TRUE,
  increase.parents = FALSE,
  clone_names = NA
)

Arguments

tree.mat	a phylogenetic tree matrix with two column specifying 'parent' (column 1) and child (column 2)
CCF.data	a table of clone CCFs with column 1 (named 'clone') specifying clone names and column 2 (name 'CCF') specifying CCFs as either fractions or percentages
warning.limit	If CCF of daughters is significantly > than the parent this may indicate the tree is incorrect. This parameter specified the ratio of daughter : parent CCFs that will trigger a warning. Default is set to 1 hence any parent with daughters > its CCF will trigger a warning (indicating how much greater the daughter CCF is than the parent)
parent.adjust	what fraction of parent to increase daughters to, default is 1
decrease.daughters	Do you want to decrease the daughter CCF to account for instances where daughter CCF > parent CCF
increase.parents	Do you want to increase the parent CCF to account for instances where daughter CCF > parent CCF

amf71/cloneMap documentation built on Jan. 11, 2024, 5:28 a.m.