# Error correction tool for noisy genotyping by sequencing (GBS) data

## Documentation for package ‘GBScleanR’ version 2.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E G H I L M N P R S T V

## -- A --

addScheme | #' Build a GbsrScheme object
addScheme-method | #' Build a GbsrScheme object
assignScheme | Assign member IDs to samples
assignScheme-method | Assign member IDs to samples

## -- B --

boxplotGBSR | Draw boxplots of specified statistics

## -- C --

closeGDS | Close the connection to the GDS file
closeGDS-method | Close the connection to the GDS file
countGenotype | Count genotype calls and alleles per sample and per marker.
countGenotype-method | Count genotype calls and alleles per sample and per marker.
countRead | Count reads per sample and per marker.
countRead-method | Count reads per sample and per marker.

## -- E --

estGeno | Genotype estimation using a hiden Morkov model
estGeno-method | Genotype estimation using a hiden Morkov model

## -- G --

gbsrGDS2CSV | Write a CSV file based on data in a GDS file
gbsrGDS2CSV-method | Write a CSV file based on data in a GDS file
gbsrGDS2VCF | Write a VCF file based on data in a GDS file
gbsrGDS2VCF-method | Write a VCF file based on data in a GDS file
GbsrGenotypeData | Class GbsrGenotypeData
GbsrGenotypeData-class | Class GbsrGenotypeData
GbsrScheme | Class 'GbsrScheme'
GbsrScheme-class | Class 'GbsrScheme'
gbsrVCF2GDS | Convert a VCF file to a GDS file
getAllele | Obtain reference allele information of markers
getAllele-method | Obtain reference allele information of markers
getChromosome | Obtain chromosome IDs of markers
getChromosome-method | Obtain chromosome IDs of markers
getCountAlleleAlt | Obtain total alternative allele counts per SNP or per sample
getCountAlleleAlt-method | Obtain total alternative allele counts per SNP or per sample
getCountAlleleMissing | Obtain total missing allele counts per SNP or per sample
getCountAlleleMissing-method | Obtain total missing allele counts per SNP or per sample
getCountAlleleRef | Obtain total reference allele counts per SNP or per sample
getCountAlleleRef-method | Obtain total reference allele counts per SNP or per sample
getCountGenoAlt | Obtain total alternative genotype counts per SNP or per sample
getCountGenoAlt-method | Obtain total alternative genotype counts per SNP or per sample
getCountGenoHet | Obtain total heterozygote counts per SNP or per sample
getCountGenoHet-method | Obtain total heterozygote counts per SNP or per sample
getCountGenoMissing | Obtain total missing genotype counts per SNP or per sample
getCountGenoMissing-method | Obtain total missing genotype counts per SNP or per sample
getCountGenoRef | Obtain total reference genotype counts per SNP or per sample
getCountGenoRef-method | Obtain total reference genotype counts per SNP or per sample
getCountRead | Obtain total read counts per SNP or per sample
getCountRead-method | Obtain total read counts per SNP or per sample
getCountReadAlt | Obtain total alternative read counts per SNP or per sample
getCountReadAlt-method | Obtain total alternative read counts per SNP or per sample
getCountReadRef | Obtain total reference read counts per SNP or per sample
getCountReadRef-method | Obtain total reference read counts per SNP or per sample
getFixedParameter | Get fixed allele read biases and mismapping rate
getFixedParameter-method | Get fixed allele read biases and mismapping rate
getGenotype | Get genotype call data.
getGenotype-method | Get genotype call data.
getHaplotype | Get haplotype call data.
getHaplotype-method | Get haplotype call data.
getInfo | Obtain information stored in the "annotation/info" node
getInfo-method | Obtain information stored in the "annotation/info" node
getMAC | Obtain minor allele counts per SNP or per sample
getMAC-method | Obtain minor allele counts per SNP or per sample
getMAF | Obtain minor allele frequencies per SNP or per sample
getMAF-method | Obtain minor allele frequencies per SNP or per sample
getMarID | Obtain the marker IDs
getMarID-method | Obtain the marker IDs
getMeanReadAlt | Obtain mean values of total alternative read counts per SNP or per sample
getMeanReadAlt-method | 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
getMeanReadRef-method | 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
getMedianReadAlt-method | 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
getMedianReadRef-method | Obtain quantile values of total reference read counts per SNP or per sample
getParents | Get parental sample information
getParents-method | Get parental sample information
getPloidy | Get ploidy
getPloidy-method | Get ploidy
getPosition | Obtain marker positions
getPosition-method | Obtain marker positions
getRead | Get read count data.
getRead-method | Get read count data.
getReplicates | Get identifiers to indicates which samples are replicates.
getReplicates-method | Get identifiers to indicates which samples are replicates.
getSamID | Obtain the sample IDs
getSamID-method | Obtain the sample IDs
getSDReadAlt | Obtain standard deviations of total alternative read counts per SNP or per sample
getSDReadAlt-method | 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
getSDReadRef-method | Obtain standard deviations of total reference read counts per SNP or per sample

## -- H --

histGBSR | Draw histograms of specified statistics

## -- I --

initScheme | Build a GbsrScheme object
initScheme-method | Build a GbsrScheme object
isOpenGDS | Check if a GDS file has been opened or not.
isOpenGDS-method | Check if a GDS file has been opened or not.

## -- L --

loadGDS | Load a GDS file and construct a GbsrGenotypeData object.

## -- M --

makeScheme | Automate a GbsrScheme object building.
makeScheme-method | Automate a GbsrScheme object building.

## -- N --

nmar | Return the number of SNPs.
nmar-method | Return the number of SNPs.
nsam | Return the number of samples.
nsam-method | Return the number of samples.

## -- P --

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.

## -- R --

reopenGDS | Reopen the connection to the GDS file.
reopenGDS-method | Reopen the connection to the GDS file.
resetCallFilter | Set the origina; data to be used in GBScleanR's functions
resetCallFilter-method | Set the origina; data to be used in GBScleanR's functions
resetFilter | Reset all filters made by 'setSamFilter()', 'setMarFilter()', and 'setCallFilter()'.
resetFilter-method | Reset all filters made by 'setSamFilter()', 'setMarFilter()', and 'setCallFilter()'.
resetMarFilter | Reset the filter made by 'setMarFilter()'
resetMarFilter-method | Reset the filter made by 'setMarFilter()'
resetSamFilter | Reset the filter made by 'setSamFilter()'
resetSamFilter-method | Reset the filter made by 'setSamFilter()'

## -- S --

setCallFilter | Filter out each genotype call meeting criteria
setCallFilter-method | Filter out each genotype call meeting criteria
setFixedParameter | Set fixed allele read biases and mismapping rate
setFixedParameter-method | Set fixed allele read biases and mismapping rate
setInfoFilter | Filter out markers based on marker quality metrics
setInfoFilter-method | Filter out markers based on marker quality metrics
setMarFilter | Filter out markers
setMarFilter-method | Filter out markers
setParents | Set labels to samples which should be recognized as parents of the population to be subjected to error correction.
setParents-method | Set labels to samples which should be recognized as parents of the population to be subjected to error correction.
setPloidy | Set ploidy
setPloidy-method | Set ploidy
setReplicates | Set identifiers to indicates which samples are replicates.
setReplicates-method | Set identifiers to indicates which samples are replicates.
setSamFilter | Filter out samples
setSamFilter-method | Filter out samples
showScheme | Show the information stored in a GbsrScheme object
showScheme-method | Show the information stored in a GbsrScheme object

## -- T --

thinMarker | Remove markers potentially having redundant information.
thinMarker-method | Remove markers potentially having redundant information.

## -- V --

validMar | Return a logical vector indicating which are valid SNP markers.
validMar-method | Return a logical vector indicating which are valid SNP markers.
validMar<- | Return a logical vector indicating which are valid SNP markers.
validMar<--method | Return a logical vector indicating which are valid SNP markers.
validSam | Return a logical vector indicating which are valid samples.
validSam-method | Return a logical vector indicating which are valid samples.
validSam<- | Return a logical vector indicating which are valid samples.
validSam<--method | Return a logical vector indicating which are valid samples.