environment in wich to search for data frames
and save result.
savegui
logical indicating if GUI settings should
be saved in the environment.
debug
logical indicating printing debug
information.
Details
Models the probability of drop-out P(D) using logistic
regression P(D|H) = B0 + B1*H, where 'H' is the peak height
or log(peak height). Produce a plot showing the model
prediction.
NB! There are several methods of scoring drop-out events
for regression. Currently the 'MethodX', 'Method1', and
'Method2' are endorsed by the DNA commission (see Appendix
B in ref 1). However, an alternative method is to consider
the whole locus and score drop-out if any allele is
missing.
Explanation of the methods: Dropout - all alleles are
scored according to LDT. This is pure observations and is
not used for modelling. MethodX - a random reference allele
is selected and drop-out is scored in relation to the the
partner allele. Method1 - the low molecular weight allele
is selected and drop-out is scored in relation to the
partner allele. Method2 - the high molecular weight allele
is selected and drop-out is scored in relation to the
partner allele. MethodL - drop-out is scored per locus i.e.
drop-out if any allele has dropped out.
Method X/1/2 records the peak height of the partner allele
to be used as the explanatory variable in the logistic
regression. The locus method L also do this when there has
been a drop-out, if not the the mean peak height for the
locus is used. Peak heights for the locus method are stored
in a separate column.
References
Peter Gill et.al., DNA commission of the International
Society of Forensic Genetics: Recommendations on the
evaluation of STR typing results that may include drop-out
and/or drop-in using probabilistic methods, Forensic
Science International: Genetics, Volume 6, Issue 6,
December 2012, Pages 679-688, ISSN 1872-4973,
10.1016/j.fsigen.2012.06.002.
http://www.sciencedirect.com/science/article/pii/S1872497312001354
Peter Gill, Roberto Puch-Solis, James Curran, The
low-template-DNA (stochastic) threshold-Its determination
relative to risk analysis for national DNA databases,
Forensic Science International: Genetics, Volume 3, Issue
2, March 2009, Pages 104-111, ISSN 1872-4973,
10.1016/j.fsigen.2008.11.009.
http://www.sciencedirect.com/science/article/pii/S1872497308001798