Man pages for tomoyukif/GBScleanR
Error correction tool for noisy genotyping by sequencing (GBS) data
| addScheme | #' Build a GbsrScheme object |
| assignScheme | Assign member IDs to samples |
| boxplotGBSR | Draw boxplots of specified statistics |
| 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 |
| GBScleanR | GBScleanR: A package to conduct error correction for noisy... |
| gbsrGDS2CSV | Write a CSV file based on data in a GDS file |
| gbsrGDS2VCF | Write a VCF file based on data in a GDS file |
| GbsrGenotypeData-class | Class 'GbsrGenotypeData' |
| GbsrScheme-class | Class 'GbsrScheme' |
| gbsrVCF2GDS | Convert a VCF file to a GDS file |
| getAllele | Obtain reference allele information of markers |
| getChromosome | Obtain chromosome IDs of markers |
| getCountAlleleAlt | Obtain total alternative allele counts per SNP or per sample |
| getCountAlleleMissing | Obtain total missing allele counts per SNP or per sample |
| getCountAlleleRef | Obtain total reference allele counts per SNP or per sample |
| getCountGenoAlt | Obtain total alternative genotype counts per SNP or per... |
| getCountGenoHet | Obtain total heterozygote counts per SNP or per sample |
| getCountGenoMissing | Obtain total missing genotype counts per SNP or per sample |
| getCountGenoRef | Obtain total reference genotype counts per SNP or per sample |
| getCountRead | Obtain total read counts per SNP or per sample |
| getCountReadAlt | Obtain total alternative read counts per SNP or per sample |
| getCountReadRef | Obtain total reference read counts per SNP or per sample |
| getFixedBias | Get fixed allele read biases |
| 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 sample |
| getMAF | Obtain minor allele frequencies per SNP or per sample |
| getMarID | Obtain the marker IDs |
| getMeanReadAlt | Obtain mean values of total alternative read counts per SNP... |
| getMeanReadRef | Obtain mean values of total reference read counts per SNP or... |
| getMedianReadAlt | Obtain quantile values of total alternative read counts per... |
| getMedianReadRef | Obtain quantile values of total reference read counts per SNP... |
| getParents | Get parental sample information |
| getPosition | Obtain marker positions |
| getRead | Get read count data. |
| getReplicates | Get identifiers to indicates which samples are replicates. |
| getSamID | Obtain the sample IDs |
| getSDReadAlt | Obtain standard deviations of total alternative read counts... |
| getSDReadRef | Obtain standard deviations of total reference read counts per... |
| 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. |
| makeScheme | Automate a GbsrScheme object building. |
| nmar | Return the number of SNPs. |
| nsam | Return the number of samples. |
| 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... |
| reopenGDS | Reopen the connection to the GDS file. |
| resetCallFilter | Set the origina; data to be used in GBScleanR's functions |
| resetFilter | Reset all filters made by 'setSamFilter()', 'setMarFilter()',... |
| resetMarFilter | Reset the filter made by 'setMarFilter()' |
| resetSamFilter | Reset the filter made by 'setSamFilter()' |
| setCallFilter | Filter out each genotype call meeting criteria |
| setFixedBias | Set fixed allele read biases |
| setInfoFilter | Filter out markers based on marker quality metrics |
| setMarFilter | Filter out markers |
| setParents | Set labels to samples which should be recognized as parents... |
| setReplicates | Set identifiers to indicates which samples are replicates. |
| setSamFilter | Filter out samples |
| showScheme | Show the information stored in a GbsrScheme object |
| thinMarker | Remove markers potentially having redundant information. |
| validMar | Return a logical vector indicating which are valid SNP... |
| validSam | Return a logical vector indicating which are valid samples. |
