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.
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 (100its overlap reduced (to e.g. 10