Files in tomoyukif/GBScleanR

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

R/AllClasses.R R/AllGenerics.R R/AllUtilities.R R/GBScleanR.R R/Methods-GbsrGenotypeData.R R/Methods-GbsrGenotypeData_HMM.R R/Methods-GbsrScheme.R R/PlotFunctions.R R/RcppExports.R README.md inst/NEWS.md man/GBScleanR.Rd man/GbsrGenotypeData-class.Rd man/GbsrScheme-class.Rd man/addScheme.Rd man/assignScheme.Rd man/boxplotGBSR.Rd man/closeGDS.Rd man/countGenotype.Rd man/countRead.Rd man/estGeno.Rd man/gbsrGDS2CSV.Rd man/gbsrGDS2VCF.Rd man/gbsrVCF2GDS.Rd man/getAllele.Rd man/getChromosome.Rd man/getCountAlleleAlt.Rd man/getCountAlleleMissing.Rd man/getCountAlleleRef.Rd man/getCountGenoAlt.Rd man/getCountGenoHet.Rd man/getCountGenoMissing.Rd man/getCountGenoRef.Rd man/getCountRead.Rd man/getCountReadAlt.Rd man/getCountReadRef.Rd man/getFixedBias.Rd man/getGenotype.Rd man/getHaplotype.Rd man/getInfo.Rd man/getMAC.Rd man/getMAF.Rd man/getMarID.Rd man/getMeanReadAlt.Rd man/getMeanReadRef.Rd man/getMedianReadAlt.Rd man/getMedianReadRef.Rd man/getParents.Rd man/getPosition.Rd man/getRead.Rd man/getReplicates.Rd man/getSDReadAlt.Rd man/getSDReadRef.Rd man/getSamID.Rd man/histGBSR.Rd man/initScheme.Rd man/isOpenGDS.Rd man/loadGDS.Rd man/makeScheme.Rd man/nmar.Rd man/nsam.Rd man/pairsGBSR.Rd man/plotDosage.Rd man/plotGBSR.Rd man/plotReadRatio.Rd man/reopenGDS.Rd man/resetCallFilter.Rd man/resetFilter.Rd man/resetMarFilter.Rd man/resetSamFilter.Rd man/setCallFilter.Rd man/setFixedBias.Rd man/setInfoFilter.Rd man/setMarFilter.Rd man/setParents.Rd man/setReplicates.Rd man/setSamFilter.Rd man/showScheme.Rd man/thinMarker.Rd man/validMar.Rd man/validSam.Rd tests/testthat.R tests/testthat/debug_01.R tests/testthat/test_01_getters.R tests/testthat/test_02_setters.R tests/testthat/test_03_countGenotype.R tests/testthat/test_04_countRead.R tests/testthat/test_05_filtering.R tests/testthat/test_06_gds2vcf.R tests/testthat/test_07_estGeno.R vignettes/BasicUsageOfGBScleanR.rmd