# Bioconductor Tools for Human Mitochondrial Variant Analysis

## Documentation for package ‘MTseeker’ version 1.0.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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