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

Documentation for package ‘GBScleanR’ version 1.0.0

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-- A --

addScan	Add genotype data into the GDS file
addScan-method	Add genotype data into the GDS file
addScheme	#' Build a GbsrScheme object
addScheme-method	#' Build a GbsrScheme object

-- B --

boxplotGBSR

Draw boxplots of specified statistics

-- C --

calcReadStats	Calculate mean, standard deviation, and quantile values of normalized read counts per sample and per marker.
calcReadStats-method	Calculate mean, standard deviation, and quantile values of normalized read counts per sample and per marker.
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
getAlleleA	Obtain reference allele information of each SNP marker
getAlleleA-method	Obtain reference allele information of each SNP marker
getAlleleB	Obtain alternative allele information of each SNP marker
getAlleleB-method	Obtain alternative allele information of each SNP marker
getChromosome	Obtain chromosome information of each SNP marker
getChromosome-method	Obtain chromosome information of each SNP marker
getCountAlleleAlt	Obtain total alternative allele counts per SNP or per scan (sample)
getCountAlleleAlt-method	Obtain total alternative allele counts per SNP or per scan (sample)
getCountAlleleMissing	Obtain total missing allele counts per SNP or per scan (sample)
getCountAlleleMissing-method	Obtain total missing allele counts per SNP or per scan (sample)
getCountAlleleRef	Obtain total reference allele counts per SNP or per scan (sample)
getCountAlleleRef-method	Obtain total reference allele counts per SNP or per scan (sample)
getCountGenoAlt	Obtain total alternative genotype counts per SNP or per scan (sample)
getCountGenoAlt-method	Obtain total alternative genotype counts per SNP or per scan (sample)
getCountGenoHet	Obtain total heterozygote counts per SNP or per scan (sample)
getCountGenoHet-method	Obtain total heterozygote counts per SNP or per scan (sample)
getCountGenoMissing	Obtain total missing genotype counts per SNP or per scan (sample)
getCountGenoMissing-method	Obtain total missing genotype counts per SNP or per scan (sample)
getCountGenoRef	Obtain total reference genotype counts per SNP or per scan (sample)
getCountGenoRef-method	Obtain total reference genotype counts per SNP or per scan (sample)
getCountRead	Obtain total read counts per SNP or per scan (sample)
getCountRead-method	Obtain total read counts per SNP or per scan (sample)
getCountReadAlt	Obtain total alternative read counts per SNP or per scan (sample)
getCountReadAlt-method	Obtain total alternative read counts per SNP or per scan (sample)
getCountReadRef	Obtain total reference read counts per SNP or per scan (sample)
getCountReadRef-method	Obtain total reference read counts per SNP or per scan (sample)
getFlipped	Get a logical vector indicating flipped SNP markers.
getFlipped-method	Get a logical vector indicating flipped SNP markers.
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 scan (sample)
getMAC-method	Obtain minor allele counts per SNP or per scan (sample)
getMAF	Obtain minor allele frequencies per SNP or per scan (sample)
getMAF-method	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)
getMeanReadAlt-method	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)
getMeanReadRef-method	Obtain mean values of total reference read counts per SNP or per scan (sample)
getParents	Get parental sample information
getParents-method	Get parental sample information
getPloidy	Obtain ploidy information of each SNP marker
getPloidy-method	Obtain ploidy information of each SNP marker
getPosition	Obtain physical position information of each SNP marker
getPosition-method	Obtain physical position information of each SNP marker
getQtileReadAlt	Obtain quantile values of total alternative read counts per SNP or per scan (sample)
getQtileReadAlt-method	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)
getQtileReadRef-method	Obtain quantile values of total reference read counts per SNP or per scan (sample)
getRead	Get read count data.
getRead-method	Get read count data.
getScanID	Obtain scan (sample) ID
getScanID-method	Obtain scan (sample) ID
getSDReadAlt	Obtain standard deviations of total alternative read counts per SNP or per scan (sample)
getSDReadAlt-method	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)
getSDReadRef-method	Obtain standard deviations of total reference read counts per SNP or per scan (sample)
getSnpID	Obtain SNP ID
getSnpID-method	Obtain SNP ID
getValidScan	Return a logical vector indicating which are valid scans (samples).
getValidScan-method	Return a logical vector indicating which are valid scans (samples).
getValidSnp	Return a logical vector indicating which are valid SNP markers.
getValidSnp-method	Return a logical vector indicating which are valid SNP markers.

-- H --

hasFlipped	Get a logical value indicating flipped SNP markers whether information exists.
hasFlipped-method	Get a logical value indicating flipped SNP markers whether information exists.
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.
loadScanAnnot	Load the stored ScanAnnotationDataFrame information
loadScanAnnot-method	Load the stored ScanAnnotationDataFrame information
loadSnpAnnot	Load the stored SnpAnnotationDataFrame information
loadSnpAnnot-method	Load the stored SnpAnnotationDataFrame information

-- N --

nscan	Return the number of scans (samples).
nscan-method	Return the number of scans (samples).
nsnp	Return the number of SNPs.
nsnp-method	Return the number of SNPs.

-- O --

openGDS	Open the connection to the GDS file.
openGDS-method	Open the connection to the GDS file.

-- 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 --

resetFilters	Reset all filters made by 'setScanFilter()', 'setSnpFilter()', and 'setCallFilter()'.
resetFilters-method	Reset all filters made by 'setScanFilter()', 'setSnpFilter()', and 'setCallFilter()'.
resetScanFilters	Reset the filter made by 'setScanFilter()'
resetScanFilters-method	Reset the filter made by 'setScanFilter()'
resetSnpFilters	Reset the filter made by 'setSnpFilter()'
resetSnpFilters-method	Reset the filter made by 'setSnpFilter()'

-- S --

saveScanAnnot	Write out the information stored in the ScanAnnotationDataFrame slot
saveScanAnnot-method	Write out the information stored in the ScanAnnotationDataFrame slot
saveSnpAnnot	Write out the information stored in the SnpAnnotationDataFrame slot
saveSnpAnnot-method	Write out the information stored in the SnpAnnotationDataFrame slot
setCallFilter	Filter out each genotype call meeting criteria
setCallFilter-method	Filter out each genotype call meeting criteria
setFiltGenotype	Set the filtered data to be used in GBScleanR's functions
setFiltGenotype-method	Set the filtered data to be used in GBScleanR's functions
setInfoFilter	Filter out markers based on marker quality metrics
setInfoFilter-method	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.
setParents-method	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
setRawGenotype-method	Set the origina; data to be used in GBScleanR's functions
setScanFilter	Filter out scans (samples)
setScanFilter-method	Filter out scans (samples)
setSnpFilter	Filter out markers
setSnpFilter-method	Filter out markers
setValidScan	Manually set valid scans (samples).
setValidScan-method	Manually set valid scans (samples).
setValidSnp	Manually set valid SNP markers.
setValidSnp-method	Manually set valid SNP markers.
showScheme	Show the information stored in a GbsrScheme object
showScheme-method	Show the information stored in a GbsrScheme object
subsetGDS	Create a GDS file with subset data of the current GDS file
subsetGDS-method	Create a GDS file with subset data of the current GDS file

-- T --

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