trichelab/MTseeker
Bioconductor Tools for Human Mitochondrial Variant Analysis

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Vignettes
Functions
209
Source code
45
Man pages
45
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trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis
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API

API for trichelab/MTseeker
Bioconductor Tools for Human Mitochondrial Variant Analysis

Global functions
.AAmakeColoredMatrix Source code
.addPuCoverage Source code
.addReadCounts Source code
.addRefSeq Source code
.byCell Source code
.byCellFrag Source code
.byFrag Source code
.byPos Source code
.calc_cov Source code
.cellFilter Source code
.colorCode Source code
.compCheck Source code
.cov Source code
.coverageByCell Source code
.darken Source code
.dedupe Source code
.extractBamFiles Source code
.extractCommonElts Source code
.extractCoverageRles Source code
.flattenConsequences Source code
.fragTable Source code
.fragsPerCell Source code
.getAnno Source code
.getCoding Source code
.getCodingRegions Source code
.getCov Source code
.getCoverageRle Source code
.getGeneImpacted Source code
.getGenome Source code
.getKnee Source code
.getMtPile Source code
.getPuSeqLen Source code
.getReadCounts Source code
.getReadProportions Source code
.getRefSeq Source code
.getRefSyn Source code
.grVR Source code
.halfheight Source code
.height Source code
.indelToMVR Source code
.injectVariantsIntoReference Source code
.makeColoredMatrix Source code
.nonRef Source code
.puGR Source code
.puToGR Source code
.puToMvr Source code Source code
.rCRSfilter Source code
.rCRSvsRSRS Source code
.refSeqLengths Source code
.resolveTies Source code
.reverseCigar Source code
.sanCheck Source code
.strpop Source code
.textbold Source code
.textcex Source code
.textloc Source code
.txCoverage Source code
.typeMutation Source code
.typeOfMutation Source code
.uniqueFrags Source code
.vafMatrix Source code
.variantsDF Source code
.weightedMeanCoverage Source code
MAlignments Man page Source code
MAlignments-class Man page
MAlignments-methods Man page
MAlignmentsList Man page Source code
MAlignmentsList-class Man page
MAlignmentsList-methods Man page
MTHGVS Man page Source code
MTcircos Man page Source code
MTcomplex Man page Source code
MTcoverage Man page Source code
MVRanges Man page Source code
MVRanges-class Man page
MVRanges-methods Man page
MVRangesList Man page Source code
MVRangesList-class Man page
MVRangesList-methods Man page
anno_rCRS Man page
annotation Man page
annotation,MVRanges-method Man page
byStrand Man page Source code
chrominfo.rCRS Man page
consensusString,MVRanges-method Man page
consensusString,MVRangesList-method Man page
coverage,MVRanges-method Man page
coverage,MVRangesList-method Man page
decomposeAndCalcConsequences Man page Source code
depthFilterAndHaploMask Man page Source code
encoding,MVRanges-method Man page
encoding,MVRangesList-method Man page
exportFilteredAsVcf Man page Source code
fileName,MAlignments-method Man page
fileName,MAlignmentsList-method Man page
filt,MVRanges-method Man page
filt,MVRangesList-method Man page
filterMT Man page Source code
filterMTvars Man page Source code
fixMetadata Man page Source code
fpFilter_RSRS Man page
fpFilter_Triska Man page
genMTcircos Man page Source code
genes Man page
genes,MVRanges-method Man page
genes,MVRangesList-method Man page
genesMTcircos Man page Source code
genome,MVRanges-method Man page
genome,MVRangesList-method Man page
genomeCoverage Man page
genomeCoverage,MAlignments-method Man page
genomeCoverage,MAlignmentsList-method Man page
genomeCoverage,MVRanges-method Man page
genomeCoverage,MVRangesList-method Man page
genomeLength Man page
genomeLength,MAlignments-method Man page
genomeLength,MAlignmentsList-method Man page
getAnnotations Man page
getAnnotations,MVRanges-method Man page
getAnnotations,MVRangesList-method Man page
getMT Man page Source code
getProteinImpact Man page Source code
getScReads Man page Source code
granges,MVRangesList-method Man page
haploMask Man page Source code
haplomask_whitelist Man page
hg19TorCRS Man page
importVCF Man page Source code
initMTcircos Man page Source code
injectMTVariants Man page Source code
lift_up_to_rCRS Man page Source code
locateMTvariants Man page Source code
locateVariants Man page
locateVariants,MVRanges,missing,missing-method Man page
locateVariants,MVRangesList,missing,missing-method Man page
mtAnno Man page
mtAnno.rCRS Man page
mtGenes Man page
mtGenes.rCRS Man page
newFilterMT Man page Source code
pileupMT Man page Source code
pileupXenograft Man page Source code
plot,MVRanges,ANY-method Man page
plot,MVRangesList,ANY-method Man page
plotMTCoverage Man page Source code
plotStrandedMTCoverage Man page Source code
pos,MVRanges-method Man page
predictCoding Man page
predictCoding,MVRanges,missing,missing,missing-method Man page
predictCoding,MVRangesList,missing,missing,missing-method Man page
rCRSeq Man page
rawMTreads Man page Source code
readLength Man page
readLength,MAlignments-method Man page
readLength,MAlignmentsList-method Man page
s4Methods Man page Source code
scanBamHeader,MAlignments-method Man page
scanBamHeader,MAlignmentsList-method Man page
scanMT Man page Source code
show,MAlignments-method Man page
show,MAlignmentsList-method Man page
show,MVRanges-method Man page
show,MVRangesList-method Man page
snpCall Man page
snpCall,MVRanges-method Man page
snpCall,MVRangesList-method Man page
summarizeVariants Man page
summarizeVariants,MVRanges,missing,missing-method Man page
summarizeVariants,MVRangesList,missing,missing-method Man page
type,MVRanges-method Man page
validMetadata Man page Source code
vcf2mvrl Man page Source code
trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.

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