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

Documentation for package ‘GBScleanR’ version 2.3.1

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-- 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.