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 |