Bioconductor Tools for Human Mitochondrial Variant Analysis


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Documentation for package ‘MTseeker’ version 1.0.6

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annotation-method wrap a VRanges for mitochondrial use
anno_rCRS annotation for the regions (genic and not) of the rCRS mitogenome
byStrand simple helper function to split a *RangesList by the strand of its mt target
callMT call mitochondrial variants against rCRS from an MAlignments[List] object
callMTVars call mitochondrial variants against rCRS from an MAlignments[List] object
chrominfo.rCRS Sequence information (seqinfo) for the rCRS mitogenome
consensusString-method wrap a VRanges for mitochondrial use
consensusString-method Wrap a VRangesList for mitochondrial use.
coverage-method wrap a VRanges for mitochondrial use
coverage-method Wrap a VRangesList for mitochondrial use.
encoding-method wrap a VRanges for mitochondrial use
encoding-method Wrap a VRangesList for mitochondrial use.
fileName-method wrap a GAlignments for easier stats
fileName-method wrap a GAlignmentsList for viewing
filt-method wrap a VRanges for mitochondrial use
filt-method Wrap a VRangesList for mitochondrial use.
filterMT Filter SummarizedExperiment or DataFrame values based on its $mtCovg column
filterMTvars sanitize PASSing mitochondrial variant calls to a moderate degree
fixMetadata fix metadata for an MAlignmentsList or MVRangesList, if needed and possible.
fpFilter_RSRS false positive filter (fpFilter) for RSRS haplogroup-determining variants
fpFilter_Triska a false positive (fp) filter from Petr Triska's manuscript on mtDNA variants
genes wrap a VRanges for mitochondrial use
genes-method wrap a VRanges for mitochondrial use
genes-method Wrap a VRangesList for mitochondrial use.
genome-method wrap a VRanges for mitochondrial use
genome-method Wrap a VRangesList for mitochondrial use.
genomeCoverage wrap a GAlignments for easier stats
genomeCoverage-method wrap a GAlignmentsList for viewing
genomeCoverage-method wrap a VRanges for mitochondrial use
genomeCoverage-method Wrap a VRangesList for mitochondrial use.
genomeLength wrap a GAlignments for easier stats
genomeLength-method wrap a GAlignments for easier stats
getAnnotations wrap a VRanges for mitochondrial use
getAnnotations-method wrap a VRanges for mitochondrial use
getAnnotations-method Wrap a VRangesList for mitochondrial use.
getMT grab the mitochondrial reads from a BAM & estimate their fraction (of total)
granges-method Wrap a VRangesList for mitochondrial use.
hg19TorCRS a liftOver chain for hg19 to rCRS attempts. We do not recommend this.
indexMTGenome build and install GmapGenome.[organism].[mtGenome], currently Hsapiens.rCRS
injectMTVariants Inject (one or more) variants against rCRS.
locateVariants wrap a VRanges for mitochondrial use
locateVariants-method wrap a VRanges for mitochondrial use
locateVariants-method Wrap a VRangesList for mitochondrial use.
MAlignments wrap a GAlignments for easier stats
MAlignments-class wraps a GAlignments with information about coverage and its target BAM file
MAlignments-methods wrap a GAlignments for easier stats
MAlignmentsList wrap a GAlignmentsList for viewing
MAlignmentsList-class wraps a GAlignmentsList (made up of MAlignments) for nicer viewing
MAlignmentsList-methods wrap a GAlignmentsList for viewing
mtAnno annotation for the rCRS genome
mtAnno.rCRS annotation for the rCRS genome
MTcircos plot a canonical human (or, in principle, any) mitochondrial genome
MTcomplex plot the (putative) functional impact of mutations to ETP genes as SVG
MTcoverage Mitochondrial genome coverage and plots for MAlignments or MVRanges objects
mtGenes Base sequences of mitochondrial coding genes.
mtGenes.rCRS All annotated gene regions (not just coding genes) from rCRS.
MTHGVS convert mitochondrial variant calls to HGVS format for naming
MVRanges wrap a VRanges for mitochondrial use
MVRanges-class like a VRanges, but for mitochondria
MVRanges-methods wrap a VRanges for mitochondrial use
MVRangesList Wrap a VRangesList for mitochondrial use.
MVRangesList-class like a VRangesList, but for mitochondria
MVRangesList-methods Wrap a VRangesList for mitochondrial use.
plot-method wrap a VRanges for mitochondrial use
plot-method Wrap a VRangesList for mitochondrial use.
plotMTCoverage Mitochondrial genome coverage and plots for MAlignments or MVRanges objects
plotStrandedMTCoverage Mitochondrial genome coverage and plots for MAlignments or MVRanges objects
pos-method wrap a VRanges for mitochondrial use
predictCoding wrap a VRanges for mitochondrial use
predictCoding-method wrap a VRanges for mitochondrial use
predictCoding-method Wrap a VRangesList for mitochondrial use.
rCRSeq The complete sequence of the human rCRS mitogenome. Yes, it's that small.
readLength wrap a GAlignments for easier stats
readLength-method wrap a GAlignments for easier stats
readLength-method wrap a GAlignmentsList for viewing
s4Methods List all defined methods for an S4 class (or classes, if you must)
scanBamHeader-method wrap a GAlignments for easier stats
show-method wrap a GAlignments for easier stats
show-method wrap a GAlignmentsList for viewing
show-method wrap a VRanges for mitochondrial use
show-method Wrap a VRangesList for mitochondrial use.
snpCall-method wrap a VRanges for mitochondrial use
snpCall-method Wrap a VRangesList for mitochondrial use.
summarizeVariants-method wrap a VRanges for mitochondrial use
summarizeVariants-method Wrap a VRangesList for mitochondrial use.
Summary-method wrap a GAlignments for easier stats
Summary-method wrap a GAlignmentsList for viewing
tallyVariants-method wrap a VRanges for mitochondrial use
type-method wrap a VRanges for mitochondrial use
validMetadata Ensure that the metadata caches in MAlignmentsLists and MVRangesLists are OK