GbsrGenotypeData-class
                        Class GbsrGenotypeData
GbsrScheme-class        Class 'GbsrScheme'
addScheme               #' Build a GbsrScheme object
assignScheme            Assign member IDs to samples
boxplotGBSR             Draw boxplots of specified statistics
closeGDS                Close the connection to the GDS file
countGenotype           Count genotype calls and alleles per sample and
                        per marker.
countRead               Count reads per sample and per marker.
estGeno                 Genotype estimation using a hiden Morkov model
gbsrGDS2CSV             Write a CSV file based on data in a GDS file
gbsrGDS2VCF             Write a VCF file based on data in a GDS file
gbsrVCF2GDS             Convert a VCF file to a GDS file
getAllele               Obtain reference allele information of markers
getChromosome           Obtain chromosome IDs of markers
getCountAlleleAlt       Obtain total alternative allele counts per SNP
                        or per sample
getCountAlleleMissing   Obtain total missing allele counts per SNP or
                        per sample
getCountAlleleRef       Obtain total reference allele counts per SNP or
                        per sample
getCountGenoAlt         Obtain total alternative genotype counts per
                        SNP or per sample
getCountGenoHet         Obtain total heterozygote counts per SNP or per
                        sample
getCountGenoMissing     Obtain total missing genotype counts per SNP or
                        per sample
getCountGenoRef         Obtain total reference genotype counts per SNP
                        or per sample
getCountRead            Obtain total read counts per SNP or per sample
getCountReadAlt         Obtain total alternative read counts per SNP or
                        per sample
getCountReadRef         Obtain total reference read counts per SNP or
                        per sample
getFixedParameter       Get fixed allele read biases and mismapping
                        rate
getGenotype             Get genotype call data.
getHaplotype            Get haplotype call data.
getInfo                 Obtain information stored in the
                        "annotation/info" node
getMAC                  Obtain minor allele counts per SNP or per
                        sample
getMAF                  Obtain minor allele frequencies per SNP or per
                        sample
getMarID                Obtain the marker IDs
getMeanReadAlt          Obtain mean values of total alternative read
                        counts per SNP or per sample
getMeanReadRef          Obtain mean values of total reference read
                        counts per SNP or per sample
getMedianReadAlt        Obtain quantile values of total alternative
                        read counts per SNP or per sample
getMedianReadRef        Obtain quantile values of total reference read
                        counts per SNP or per sample
getParents              Get parental sample information
getPloidy               Get ploidy
getPosition             Obtain marker positions
getRead                 Get read count data.
getReplicates           Get identifiers to indicates which samples are
                        replicates.
getSDReadAlt            Obtain standard deviations of total alternative
                        read counts per SNP or per sample
getSDReadRef            Obtain standard deviations of total reference
                        read counts per SNP or per sample
getSamID                Obtain the sample IDs
histGBSR                Draw histograms of specified statistics
initScheme              Build a GbsrScheme object
isOpenGDS               Check if a GDS file has been opened or not.
loadGDS                 Load a GDS file and construct a
                        GbsrGenotypeData object.
makeScheme              Automate a GbsrScheme object building.
nmar                    Return the number of SNPs.
nsam                    Return the number of samples.
pairsGBSR               Draw a scatter plot of a pair of specified
                        statistics
plotDosage              Draw line plots of allele dosage per marker per
                        sample.
plotGBSR                Draw line plots of specified statistics
plotReadRatio           Draw line plots of proportion of reference
                        allele read counts per marker per sample.
reopenGDS               Reopen the connection to the GDS file.
resetCallFilter         Set the origina; data to be used in GBScleanR's
                        functions
resetFilter             Reset all filters made by 'setSamFilter()',
                        'setMarFilter()', and 'setCallFilter()'.
resetMarFilter          Reset the filter made by 'setMarFilter()'
resetSamFilter          Reset the filter made by 'setSamFilter()'
setCallFilter           Filter out each genotype call meeting criteria
setFixedParameter       Set fixed allele read biases and mismapping
                        rate
setInfoFilter           Filter out markers based on marker quality
                        metrics
setMarFilter            Filter out markers
setParents              Set labels to samples which should be
                        recognized as parents of the population to be
                        subjected to error correction.
setPloidy               Set ploidy
setReplicates           Set identifiers to indicates which samples are
                        replicates.
setSamFilter            Filter out samples
showScheme              Show the information stored in a GbsrScheme
                        object
thinMarker              Remove markers potentially having redundant
                        information.
validMar                Return a logical vector indicating which are
                        valid SNP markers.
validSam                Return a logical vector indicating which are
                        valid samples.
