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

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Vignettes
Functions
230
Source code
18
Man pages
67
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tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data
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API

API for tomoyukif/GBScleanR
Error correction tool for noisy genotyping by sequencing (GBS) data

Global functions
.applySampleCallFilter Source code
.bindErrors Source code
.boxplot.maker Source code
.calcErrors Source code
.calcMissmap Source code
.calcNextJnum Source code
.calcReadBias Source code
.calcSubFilter Source code
.checkArgValid Source code
.checkCallArgValid Source code
.checkDefault Source code
.checkInfoArgValid Source code
.checkNodes Source code
.checkPread Source code
.checkScheme Source code
.cleanEachChr Source code
.compareValues Source code
.compressNodes Source code
.countGeno Source code
.countRead Source code
.create_gdsn Source code
.df.maker Source code
.filtData Source code
.flipParam Source code
.gds_comp Source code
.gds_decomp Source code
.getBestSeq Source code
.getBias Source code
.getInitProb Source code
.getJnum Source code
.getParams Source code
.getParentGenotype Source code
.getPedigree Source code
.getPossibleGeno Source code
.getPossibleHap Source code
.getStatsData Source code
.getValidPat Source code
.getXoFreq Source code
.halfJoint Source code
.hap2geno Source code
.hist.maker Source code
.initGDS Source code
.initJnum Source code
.initialPattern Source code
.lab.maker Source code
.limit.maker Source code
.loadReadCounts Source code
.makeCallFilterData Source code
.makeFilter Source code
.makeGenoParents Source code
.makeGenoPat Source code
.makeInfoFilter Source code
.makePattern Source code
.makeStatsFilter Source code
.minimizeRecombination Source code
.modGDS Source code
.orderParents Source code
.pGenoFilt Source code
.pairs.maker Source code
.parentPat2Geno Source code
.parseGBSRformat Source code
.pat2hap Source code
.pileupAD Source code
.plot.maker Source code
.progenyPattern Source code
.putAttrGdsn Source code
.recalcGT Source code
.replaceGT Source code
.runCycle Source code
.saveADB Source code
.saveEDS Source code
.saveGeno Source code
.saveHap Source code
.saveMR Source code
.savePGeno Source code
.setThreads Source code
.solveBorderConflict Source code
.sumUpBias Source code
.summarizeEst Source code
.transitionProb Source code
.validMating Source code
GBScleanR Man page
GBScleanR-package Man page
GbsrGenotypeData Man page
GbsrGenotypeData-class Man page
GbsrScheme Man page
GbsrScheme-class Man page
addScheme Man page
addScheme,GbsrGenotypeData-method Man page
addScheme,GbsrScheme-method Man page
assignScheme Man page
assignScheme,GbsrGenotypeData-method Man page
assignScheme,GbsrScheme-method Man page
boxplotGBSR Man page Source code
closeGDS Man page
closeGDS,GbsrGenotypeData-method Man page
countGenotype Man page
countGenotype,GbsrGenotypeData-method Man page
countRead Man page
countRead,GbsrGenotypeData-method Man page
count_geno Source code
count_read Source code
estGeno Man page
estGeno,GbsrGenotypeData-method Man page
gbsrGDS2CSV Man page
gbsrGDS2CSV,GbsrGenotypeData-method Man page
gbsrGDS2VCF Man page
gbsrGDS2VCF,GbsrGenotypeData-method Man page
gbsrVCF2GDS Man page Source code
getAllele Man page
getAllele,GbsrGenotypeData-method Man page
getChromosome Man page
getChromosome,GbsrGenotypeData-method Man page
getCountAlleleAlt Man page
getCountAlleleAlt,GbsrGenotypeData-method Man page
getCountAlleleMissing Man page
getCountAlleleMissing,GbsrGenotypeData-method Man page
getCountAlleleRef Man page
getCountAlleleRef,GbsrGenotypeData-method Man page
getCountGenoAlt Man page
getCountGenoAlt,GbsrGenotypeData-method Man page
getCountGenoHet Man page
getCountGenoHet,GbsrGenotypeData-method Man page
getCountGenoMissing Man page
getCountGenoMissing,GbsrGenotypeData-method Man page
getCountGenoRef Man page
getCountGenoRef,GbsrGenotypeData-method Man page
getCountRead Man page
getCountRead,GbsrGenotypeData-method Man page
getCountReadAlt Man page
getCountReadAlt,GbsrGenotypeData-method Man page
getCountReadRef Man page
getCountReadRef,GbsrGenotypeData-method Man page
getGenotype Man page
getGenotype,GbsrGenotypeData-method Man page
getHaplotype Man page
getHaplotype,GbsrGenotypeData-method Man page
getInfo Man page
getInfo,GbsrGenotypeData-method Man page
getMAC Man page
getMAC,GbsrGenotypeData-method Man page
getMAF Man page
getMAF,GbsrGenotypeData-method Man page
getMarID Man page
getMarID,GbsrGenotypeData-method Man page
getMeanReadAlt Man page
getMeanReadAlt,GbsrGenotypeData-method Man page
getMeanReadRef Man page
getMeanReadRef,GbsrGenotypeData-method Man page
getMedianReadAlt Man page
getMedianReadAlt,GbsrGenotypeData-method Man page
getMedianReadRef Man page
getMedianReadRef,GbsrGenotypeData-method Man page
getParents Man page
getParents,GbsrGenotypeData-method Man page
getPosition Man page
getPosition,GbsrGenotypeData-method Man page
getRead Man page
getRead,GbsrGenotypeData-method Man page
getReplicates Man page
getReplicates,GbsrGenotypeData-method Man page
getSDReadAlt Man page
getSDReadAlt,GbsrGenotypeData-method Man page
getSDReadRef Man page
getSDReadRef,GbsrGenotypeData-method Man page
getSamID Man page
getSamID,GbsrGenotypeData-method Man page
get_genocall Source code
histGBSR Man page Source code
initScheme Man page
initScheme,GbsrGenotypeData-method Man page
initScheme,GbsrScheme-method Man page
isOpenGDS Man page
isOpenGDS,GbsrGenotypeData-method Man page
loadGDS Man page Source code
nmar Man page
nmar,GbsrGenotypeData-method Man page
nsam Man page
nsam,GbsrGenotypeData-method Man page
pairsGBSR Man page Source code
plotDosage Man page Source code
plotGBSR Man page Source code
plotReadRatio Man page Source code
print.GbsrGenotypeData Source code
reopenGDS Man page
reopenGDS,GbsrGenotypeData-method Man page
resetCallFilter Man page
resetCallFilter,GbsrGenotypeData-method Man page
resetFilter Man page
resetFilter,GbsrGenotypeData-method Man page
resetMarFilter Man page
resetMarFilter,GbsrGenotypeData-method Man page
resetSamFilter Man page
resetSamFilter,GbsrGenotypeData-method Man page
run_fb Source code
run_viterbi Source code
setCallFilter Man page
setCallFilter,GbsrGenotypeData-method Man page
setInfoFilter Man page
setInfoFilter,GbsrGenotypeData-method Man page
setMarFilter Man page
setMarFilter,GbsrGenotypeData-method Man page
setParents Man page
setParents,GbsrGenotypeData-method Man page
setReplicates Man page
setReplicates,GbsrGenotypeData-method Man page
setSamFilter Man page
setSamFilter,GbsrGenotypeData-method Man page
showScheme Man page
showScheme,GbsrGenotypeData-method Man page
showScheme,GbsrScheme-method Man page
thinMarker Man page
thinMarker,GbsrGenotypeData-method Man page
thinout_marker Source code
validMar Man page
validMar,GbsrGenotypeData-method Man page
validMar<- Man page
validMar<-,GbsrGenotypeData-method Man page
validSam Man page
validSam,GbsrGenotypeData-method Man page
validSam<- Man page
validSam<-,GbsrGenotypeData-method Man page
tomoyukif/GBScleanR documentation built on May 7, 2024, 6:53 p.m.

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