Visualizes the scoring and binning of microsatellite fragment sizes

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Documentation for package ‘MsatAllele’ version 1.05

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MsatAllele-package Visualizes and scores microsatellite alleles from electrophoresis fragment sizes
AlleleCum Plots a cumulative allele size distribution
AlleleHist Plots an histogram of microsatellite fragment sizes
bin.limits Writes the limits of bin classes and rounded bin codes
BinStat Summary bin statistics
DBase A data base of the type used by this package
DBZn A data base of the type used by this package with Zostera noltii data
DefBinLim Lets the used define bin limits
get.allele Gets the allele code from an electrophoresis fragment size
getpoints Interacts with AlleleCum graph to list observations
InputFile A data matrix similar to the tab delimited text file such as needed to data input
mark.bins Adds bin limits to histograms of fragment size distribution
MsatAllele Visualizes and scores microsatellite alleles from electrophoresis fragment sizes
OrderByLocus A function to order the fragment size vector for a given locus
read.ah.file Reads .ah files from Strand and creates a R data base
read.frag.sizes Reads tab delimited text files with input fragment sizes creates a R data base
restrict.hist Plots an histogram of a restricted range of microsatellite fragment sizes
STRandOUT A table like the one exported in the Strand .ah file
subdataBase Sorts the data base for a given locus and a restricted range
transDB Creates a data base object in the form used by other functions in the package
write.data Write multilocus genotype tables allowing to specify the use of manual or automatic binning methods
write.PG.file.all Writes a file with the bin codes with one column per allele
write.PG.file.loc Writes a file with the bin codes with one column per locus