API for gschofl/DR2S
Dual redundant reference sequencing

Global functions
%>% Man page
.generateReferenceSequence Man page
.getIdleCores Man page
CLS Source code
CLS.HapPart Man page Source code
CODE_MAP Source code
CODE_PATTERN Source code
COL_PATTERN Source code
Consmat_ Source code
DNA_BASES Source code
DNA_PROB Source code
DR2S Man page
DR2S-package Man page
DR2S_ Man page
HLA_LOCI Source code
HTR Source code
HTR.HapPart Man page Source code
HapPart Man page Source code
InitDR2S Man page Source code
InitDR2S.DR2Sconf Source code
K Source code
K.HapPart Man page Source code
KIR_LOCI Source code
LR_PIPELINE Source code
MANDATORY_CONF_FIELDS Source code
MANDATORY_OPTS Source code
MapList_ Source code
MergeEnv Man page Source code
MergeEnv_ Man page
NUCCOL Source code
OC Source code
OC.HapPart Man page Source code
ORDERED_CONF_FIELDS Source code
OVL Source code
PARTCOL Source code
PRT Source code
PRT.HapPart Man page Source code
PSDM Source code
PWM Source code
PWM.HapPart Man page Source code
PWMscore Source code
Pileup_ Source code
SCR Source code
SCR.HapPart Man page Source code
SNP Source code
SNP.HapPart Man page Source code
SNPmatrix Man page Source code
SQS Source code
SQS.HapPart Man page Source code
SR_PIPELINE Source code
VALID_DNA Source code
ambiguousPositions Source code
ambiguousPositions.NULL Source code
ambiguousPositions.consmat Source code
ambiguousPositions.pileup Source code
as.data.frame.consmat Source code
as.matrix.consmat Source code
associationMatrix Source code
bamSortIndex Source code
bampath Man page Source code
bampath.MapList Source code
bampath.pileup Source code
browseAlign Source code
browseSeqs Source code
bwamemCmd Source code
cache Man page Source code
cache.DR2S Source code
camelCasify Source code
capitalise Source code
checkAlignmentFile Man page Source code
checkClusterMerge Source code
checkCoverage Source code
checkHomopolymerCount Man page Source code
checkReportStatus Source code
checkSRScoring Source code
clear Man page Source code
clear.DR2S Source code
clusterPolymorphicPositions Source code
collapseHomopolymers Source code
collapsePairLines_ Source code
collectPileupParams Source code
colon Source code
comma Source code
compact Source code
confLog Source code
conseq Man page Source code
conseq.matrix Source code
conseq.pileup Source code
consmat Man page Source code
consmat.MapList Source code
consmat.consmat Source code
consmat.matrix Source code
consmat.pileup Source code
consmat.tbl_df Source code
consmat<- Man page
consname Man page Source code
consname.MapList Source code
conspath Man page Source code
conspath.MapList Source code
coordRadar Source code
correlogram Source code
coverage Source code
cpp_PSDM Source code
cpp_hamming Source code
cpp_polymorphicPositions Source code
cpp_top2Cols Source code
cramerV Source code
createDR2SConf Man page Source code Source code
createIgvConfigs Man page Source code
createIgvJsFiles Man page Source code
createPWM Man page Source code
cropOutdir Source code
cropPath Source code
dirCreateIfNotExists Source code
disambiguateVariant Man page Source code
distributeGaps Source code
doUpdate_ Source code
dot Source code
editor Source code
equaliseConsmat Source code
expandAllele Source code
expandDR2SConf Source code
expandLongreadConsmat Source code
extractAmbigLetters Source code
extractFastq Source code
extractIdsFromMat Source code
extractInsertion Source code
extractVariant_ Source code
fileDeleteIfExists Source code
filterReads Source code
filterVariant Source code
findChimeric Source code
findCutpoint Source code
findReads Source code
findRef Source code
finishCn1 Source code
fragmentReads Source code
generateMappingCommands Source code
generateReferenceSequence Source code
getCl Source code
getClusts Source code
getGapErrorBackground Source code
getIdleCores Source code
getInsertions Source code
getMinLenClust Source code
getModeValue Source code
getSRPartitionScores Man page Source code
getScores Source code
getSeqsFromMat Source code
getUpdatedSeqs Source code
getVariants Source code
hammingDist Man page Source code
hasCommand Source code
incr Source code
incr.indenter Source code
indelRate Man page Source code
indelRate.pileup Source code
indelRate<- Man page
indentation Source code
initialiseDR2S Source code
ins Man page Source code
ins.consmat Source code
ins<- Man page
is.freq Man page Source code
is.freq.consmat Source code
litArrows Source code
litQuote Source code
locationShift Source code
lvl Source code
lvl.indenter Source code
makeAmbigConsensus_ Source code
makeOpts Source code
makeProbConsensus_ Source code
makeSimpleConsensus_ Source code
mapFinal Man page Source code
mapFinal.DR2S Source code
mapInit Man page Source code
mapInit.DR2S Source code
mapInitSR Source code
mapIter Man page Source code
mapIter.DR2S Source code
mapReads Source code
mapSoftclip Source code
mat2rle Source code
mcoef Source code
mcoef.HapPart Man page Source code
mergeList Source code
meta Man page Source code
meta.MapList Source code
meta.pileup Source code
minimapCmd Source code
msaFromBam Source code
n Man page Source code
n.consmat Source code
n<- Man page
normaliseDR2SConf Source code
normaliseLocus Source code
normaliseLongreads Source code
normaliseOpts Source code
normaliseShortreads Source code
offsetBases Man page Source code
offsetBases.consmat Source code
offsetBases<- Man page
onLoad Source code
optimalPartitionLimits Source code
optstring Source code
partRead Source code
partition Source code
partition.HapPart Source code
partitionLongreads Man page Source code
partitionLongreads.DR2S Source code
partitionReads Man page Source code
partitionShortreads Man page Source code
partitionShortreads.DR2S Source code
pdHla Source code
pdKir Source code
pickReads Source code
pickTopXReads Source code
pileup Man page Source code
pileupFindInsertionPositions_ Source code
pileupGetInsertions_ Source code
pileupIncludeInsertions Source code
plotDiagnosticAlignment Man page Source code
plotPartitionHistogram Man page Source code
plotPartitionHistogramMulti Man page Source code
plotPartitionTree Man page Source code
plotPileupBasecallFrequency Man page Source code
plotPileupCoverage Man page Source code
plotRadarPartition Man page Source code
polish Man page Source code
polish.DR2S Source code
polymorphicPositions Man page Source code
polymorphicPositions.consmat Source code
polymorphicPositions.pileup Source code
print.DR2Sconf Source code
print.HapList Source code
print.HapPart Source code
print.MapList Source code
print.PartList Source code
print.consmat Source code
print.pileup Source code
print.variant Source code
print.variantList Source code
readDR2S Man page Source code
readDR2SConf Man page Source code
readMSA Man page Source code
readPairFile Source code
read_score Source code
readpath Man page Source code
readpath.MapList Source code
reads Man page Source code
reads.pileup Source code
reads<- Man page
readtype Man page Source code
readtype.MapList Source code
readtype.pileup Source code
reexports Man page
refineAlignment Man page Source code
refname Man page Source code
refname.MapList Source code
refname.pileup Source code
refpath Man page Source code
refpath.MapList Source code
refpath.pileup Source code
report Man page Source code
report.DR2S Source code
reportCheckedConsensus Man page Source code
reportMap_ Source code
rescale Source code
runbwamem Source code
runminimap Source code
scoreHighestSR Man page Source code
selectAssociatedPolymorphicPositions Source code
semicolon Source code
seq2rle Source code
setRunstats Source code
stats Man page Source code
stats.MapList Source code
stats.pileup Source code
strip Source code
stripIndel Source code
strsplit1 Source code
strsplitN Source code
subSampleBam Man page Source code
suppressGaps_ Source code
tag Man page Source code
tag.MapList Source code
trimPolymorphicEnds Source code
trimSoftclippedEnds Source code
underscore Source code
updateDR2SConf Source code
validateOpts Source code
variant Source code
wrap Source code
writeCheckConsensus Source code
writeConseq Source code
writeDR2SConf Man page Source code
writeMSA Man page Source code
writePartFq Source code
writeRefineAlignments Source code
writeReportCheckedConsensus Source code
yield Source code
yield.HapEnv Source code
gschofl/DR2S documentation built on Dec. 19, 2018, 8:04 a.m.