calculateOverlap: Calculate Bins Overlap

View source: R/calculateOverlap.r

calculateOverlapR Documentation

Calculate Bins Overlap

Description

Analyses the bins overlap between colors.

Usage

calculateOverlap(
  data,
  db = NULL,
  penalty = NULL,
  virtual = TRUE,
  debug = FALSE
)

Arguments

data

data frame providing kit information.

db

data frame allele frequency database.

penalty

vector with factors for reducing the impact from distant dye channels. NB! Length must equal number of dyes in kit minus one.

virtual

logical default is TRUE meaning that overlap calculation includes virtual bins.

debug

logical indicating printing debug information.

Details

By analyzing the bins overlap between dye channels a measure of the risk for spectral pull-up artefacts can be obtain. The default result is a matrix with the total bins overlap in number of base pairs. If an allele frequency database is provided the overlap at each bin is multiplied with the frequency of the corresponding allele. If no frequence exist for that allele a frequency of 5/2N will be used. X and Y alleles is given the frequency 1. A penalty matrix can be supplied to reduce the effect by spectral distance, meaning that overlap with the neighboring dye can be counted in full (100 while a non neighbor dye get its overlap reduced (to e.g. 10

Value

data.frame with columns 'Kit', 'Color', [dyes], 'Sum', and 'Score'.


strvalidator documentation built on July 26, 2023, 5:45 p.m.