| anno_rCRS | annotation for the regions (genic and not) of the rCRS... |
| byStrand | simple helper function to split a *RangesList by the strand... |
| chrominfo.rCRS | Sequence information (seqinfo) for the rCRS mitogenome |
| decomposeAndCalcConsequences | Decompose and annotate AA changes in MT variants |
| depthFilterAndHaploMask | process an MVRangesList for 20x depth and haplomask it note... |
| exportFilteredAsVcf | convenience wrapper for dumping filtered variants directly to... |
| filterMT | Filter SummarizedExperiment or DataFrame values based on its... |
| filterMTvars | sanitize PASSing mitochondrial variant calls to a moderate... |
| fixMetadata | fix metadata for an MAlignmentsList or MVRangesList, if... |
| fpFilter_RSRS | false positive filter (fpFilter) for RSRS... |
| fpFilter_Triska | a false positive (fp) filter from Petr Triska's manuscript on... |
| getMT | grab the mitochondrial reads from a BAM & estimate their... |
| getProteinImpact | Annotate AA changes in MT variants |
| getScReads | merge into MTseeker; could also do this with SmartSeq, etc. |
| haploMask | Mask haplogroup specific variants using haplogrep |
| haplomask_whitelist | a whitelist for haplomasking |
| hg19TorCRS | a liftOver chain for hg19 to rCRS attempts. We do not... |
| importVCF | Import a VCF directly into MTseeker |
| injectMTVariants | Inject (one or more) variants against rCRS. |
| lift_up_to_rCRS | Lift hg19 chrM to rCRS |
| locateMTvariants | Locates the variant and determines local bounds within gene... |
| MAlignments-class | wraps a GAlignments with information about coverage and its... |
| MAlignmentsList-class | wraps a GAlignmentsList (made up of MAlignments) for nicer... |
| MAlignmentsList-methods | wrap a GAlignmentsList for viewing |
| MAlignments-methods | wrap a GAlignments for easier stats |
| mtAnno | annotation for the rCRS genome |
| MTcircos | plot a canonical human (or, in principle, any) mitochondrial... |
| MTcomplex | plot the (putative) functional impact of mutations to ETP... |
| MTcoverage | Mitochondrial genome coverage and plots for MAlignments or... |
| 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-class | like a VRanges, but for mitochondria |
| MVRangesList-class | like a VRangesList, but for mitochondria |
| MVRangesList-methods | Wrap a VRangesList for mitochondrial use. |
| MVRanges-methods | wrap a VRanges for mitochondrial use |
| newFilterMT | Filter SummarizedExperiment, DataFrame, MVRanges, or... |
| pileupMT | Pileup the mitochondrial reads in a BAM, for variant calling... |
| pileupXenograft | test harness for simultaneous mouse/human MT variant calling... |
| rawMTreads | Raw reads shown as GAlignmentsList |
| rCRSeq | The complete sequence of the human rCRS mitogenome. Yes, it's... |
| s4Methods | List all defined methods for an S4 class (or classes, if you... |
| scanMT | Figure out where the mitochondrial reads in a BAM are, so we... |
| validMetadata | Ensure that the metadata caches in MAlignmentsLists and... |
| vcf2mvrl | Convert a VCF to an MVRangesList object |
