Man pages for Bioconductor/VariantAnnotation
Annotation of Genetic Variants
| defunct | Defunct Functions in Package 'VariantAnnotation' |
| filterVcf-methods | Filter VCF files |
| genotypeToSnpMatrix-methods | Convert genotype calls from a VCF file to a SnpMatrix object |
| getTranscriptSeqs-methods | Get transcript sequences |
| GLtoGP | Convert genotype likelihoods to genotype probabilities |
| indexVcf-method | Create index files for VCF files |
| isSNV-methods | Identification of genomic variant types. |
| locateVariants-methods | Locate variants |
| PolyPhenDb-class | PolyPhenDb objects |
| PolyPhenDbColumns | PolyPhenDb Columns |
| post_Hs_region | elementary vep/homo_sapiens/region call to ensembl VEP REST... |
| predictCoding-methods | Predict amino acid coding changes for variants |
| probabilityToSnpMatrix | Convert posterior genotype probability to a SnpMatrix object |
| PROVEANDb-class | PROVEANDb objects |
| readVcf-methods | Read VCF files |
| scanVcf-methods | Import VCF files |
| ScanVcfParam-class | Parameters for scanning VCF files |
| seqinfo-method | Get seqinfo for VCF file |
| SIFTDb-class | SIFTDb objects |
| SIFTDbColumns | SIFTDb Columns |
| snpSummary | Counts and distribution statistics for SNPs in a VCF object |
| summarizeVariants-methods | Summarize variants by sample |
| variant_body | helper function to construct inputs for VEP REST API |
| VariantType-class | VariantType subclasses |
| VCF-class | VCF class objects |
| VcfFile-class | Manipulate Variant Call Format (Vcf) files. |
| VCFHeader-class | VCFHeader instances |
| vep_by_region | Use the VEP region API on variant information in a VCF object... |
| VRanges-class | VRanges objects |
| VRangesList-class | VRangesList objects |
| writeVcf-methods | Write VCF files |
