GbsrGenotypeData-class
                        Class 'GbsrGenotypeData'
GbsrScheme-class        Class 'GbsrScheme'
addScan                 Add genotype data into the GDS file
addScheme               #' Build a GbsrScheme object
boxplotGBSR             Draw boxplots of specified statistics
calcReadStats           Calculate mean, standard deviation, and
                        quantile values of normalized read counts per
                        sample and per marker.
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
getAlleleA              Obtain reference allele information of each SNP
                        marker
getAlleleB              Obtain alternative allele information of each
                        SNP marker
getChromosome           Obtain chromosome information of each SNP
                        marker
getCountAlleleAlt       Obtain total alternative allele counts per SNP
                        or per scan (sample)
getCountAlleleMissing   Obtain total missing allele counts per SNP or
                        per scan (sample)
getCountAlleleRef       Obtain total reference allele counts per SNP or
                        per scan (sample)
getCountGenoAlt         Obtain total alternative genotype counts per
                        SNP or per scan (sample)
getCountGenoHet         Obtain total heterozygote counts per SNP or per
                        scan (sample)
getCountGenoMissing     Obtain total missing genotype counts per SNP or
                        per scan (sample)
getCountGenoRef         Obtain total reference genotype counts per SNP
                        or per scan (sample)
getCountRead            Obtain total read counts per SNP or per scan
                        (sample)
getCountReadAlt         Obtain total alternative read counts per SNP or
                        per scan (sample)
getCountReadRef         Obtain total reference read counts per SNP or
                        per scan (sample)
getFlipped              Get a logical vector indicating flipped SNP
                        markers.
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 scan
                        (sample)
getMAF                  Obtain minor allele frequencies per SNP or per
                        scan (sample)
getMeanReadAlt          Obtain mean values of total alternative read
                        counts per SNP or per scan (sample)
getMeanReadRef          Obtain mean values of total reference read
                        counts per SNP or per scan (sample)
getParents              Get parental sample information
getPloidy               Obtain ploidy information of each SNP marker
getPosition             Obtain physical position information of each
                        SNP marker
getQtileReadAlt         Obtain quantile values of total alternative
                        read counts per SNP or per scan (sample)
getQtileReadRef         Obtain quantile values of total reference read
                        counts per SNP or per scan (sample)
getRead                 Get read count data.
getSDReadAlt            Obtain standard deviations of total alternative
                        read counts per SNP or per scan (sample)
getSDReadRef            Obtain standard deviations of total reference
                        read counts per SNP or per scan (sample)
getScanID               Obtain scan (sample) ID
getSnpID                Obtain SNP ID
getValidScan            Return a logical vector indicating which are
                        valid scans (samples).
getValidSnp             Return a logical vector indicating which are
                        valid SNP markers.
hasFlipped              Get a logical value indicating flipped SNP
                        markers whether information exists.
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.
loadScanAnnot           Load the stored ScanAnnotationDataFrame
                        information
loadSnpAnnot            Load the stored SnpAnnotationDataFrame
                        information
nscan                   Return the number of scans (samples).
nsnp                    Return the number of SNPs.
openGDS                 Open the connection to the GDS file.
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.
resetFilters            Reset all filters made by 'setScanFilter()',
                        'setSnpFilter()', and 'setCallFilter()'.
resetScanFilters        Reset the filter made by 'setScanFilter()'
resetSnpFilters         Reset the filter made by 'setSnpFilter()'
saveScanAnnot           Write out the information stored in the
                        ScanAnnotationDataFrame slot
saveSnpAnnot            Write out the information stored in the
                        SnpAnnotationDataFrame slot
setCallFilter           Filter out each genotype call meeting criteria
setFiltGenotype         Set the filtered data to be used in GBScleanR's
                        functions
setInfoFilter           Filter out markers based on marker quality
                        metrics
setParents              Set labels to samples which should be
                        recognized as parents of the population to be
                        subjected to error correction.
setRawGenotype          Set the origina; data to be used in GBScleanR's
                        functions
setScanFilter           Filter out scans (samples)
setSnpFilter            Filter out markers
setValidScan            Manually set valid scans (samples).
setValidSnp             Manually set valid SNP markers.
showScheme              Show the information stored in a GbsrScheme
                        object
subsetGDS               Create a GDS file with subset data of the
                        current GDS file
thinMarker              Remove markers potentially having redundant
                        information.
