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