R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 26 found.
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GLtoGP (Package: VariantAnnotation) : Convert genotype likelihoods to genotype probabilities

Convert an array of genotype likelihoods to posterior genotype probabilities.

● Data Source: BioConductor
● Keywords: manip
● Alias: GLtoGP, PLtoGP
● 0 images

PROVEANDb-class (Package: VariantAnnotation) : PROVEANDb objects

The PROVEANDb class is a container for storing a connection to a PROVEAN sqlite database.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: PROVEAN, PROVEANDb, PROVEANDb-class, class:PROVEANDb
● 0 images

PolyPhenDb-class (Package: VariantAnnotation) : PolyPhenDb objects

The PolyPhenDb class is a container for storing a connection to a PolyPhen sqlite database.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: PolyPhen, PolyPhenDb, PolyPhenDb-class, class:PolyPhenDb
● 0 images

PolyPhenDbColumns (Package: VariantAnnotation) : PolyPhenDb Columns

Description of the PolyPhen Sqlite Database Columns

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: PolyPhenDbColumns
● 0 images

SIFTDb-class (Package: VariantAnnotation) : SIFTDb objects

The SIFTDb class is a container for storing a connection to a SIFT sqlite database.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: SIFT, SIFTDb, SIFTDb-class, class:SIFTDb
● 0 images

SIFTDbColumns (Package: VariantAnnotation) : SIFTDb Columns

Description of the SIFT Sqlite Database Columns

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: SIFTDbColumns
● 0 images

ScanVcfParam-class (Package: VariantAnnotation) : Parameters for scanning VCF files

Use ScanVcfParam() to create a parameter object influencing which records and fields are imported from a VCF file. Record parsing is based on genomic coordinates and requires a Tabix index file. Individual VCF elements can be specified in the ‘fixed’, ‘info’, ‘geno’ and ‘samples’ arguments.

● Data Source: BioConductor
● Keywords: classes
● Alias: ScanVcfParam, ScanVcfParam,ANY-method, ScanVcfParam,missing-method, ScanVcfParam-class, vcfFixed, vcfFixed<-, vcfGeno, vcfGeno<-, vcfInfo, vcfInfo<-, vcfSamples, vcfSamples<-, vcfTrimEmpty, vcfTrimEmpty<-, vcfWhich, vcfWhich<-
● 0 images

VCF-class (Package: VariantAnnotation) : VCF class objects

The VCF class is a virtual class extended from RangedSummarizedExperiment. The subclasses, CompressedVCF and ExtendedVCF, are containers for holding data from Variant Call Format files.

● Data Source: BioConductor
● Keywords:
● Alias: CollapsedVCF, CollapsedVCF-class, ExpandedVCF, ExpandedVCF-class, VCF-class, class:CollapsedVCF, class:ExpandedVCF, class:VCF
● 0 images

VCFHeader-class (Package: VariantAnnotation) : VCFHeader instances

The VCFHeader class holds Variant Call Format (VCF) file header information and is produced from a call to scanVcfHeader.

● Data Source: BioConductor
● Keywords:
● Alias: VCFHeader-class
● 0 images

VRanges-class (Package: VariantAnnotation) : VRanges objects

The VRanges class is a container for variant calls, including SNVs and indels. It extends GRanges to provide special semantics on top of a simple vector of genomic locations. While it is not as expressive as the VCF object, it is a simpler alternative that may be convenient for variant calling/filtering and similar exercises.

● Data Source: BioConductor
● Keywords:
● Alias: VRanges, VRanges-class, class:VRanges
● 0 images