calculateOverlap: Bins Overlap
Description
calculateOverlap 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.
Value
- data.frame with columns 'Kit', 'Color', [dyes], 'Sum', and 'Score'.
Details
By analysing 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 neighbouring dye can be counted in full (100while a non neighbour dye get its overlap reduced (to e.g. 10