R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 28 found.
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FeatureDb-class (Package: GenomicFeatures) : FeatureDb objects

The FeatureDb class is a generic container for storing genomic locations of an arbitrary type of genomic features.

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

TxDb-class (Package: GenomicFeatures) : TxDb objects

The TxDb class is a container for storing transcript annotations.

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

as-format-methods (Package: GenomicFeatures) : Coerce to file format structures

These functions coerce a TxDb object to a GRanges object with metadata columns encoding transcript structures according to the model of a standard file format. Currently, BED and GFF models are supported. If a TxDb is passed to export, when targeting a BED or GFF file, this coercion occurs automatically.

● Data Source: BioConductor
● Keywords:
● Alias: asBED,TxDb-method, asGFF,TxDb-method
● 0 images

mapToTranscripts (Package: GenomicFeatures) : Map range coordinates between transcripts and genome space

Map range coordinates between features in the transcriptome and genome (reference) space.

● Data Source: BioConductor
● Keywords: methods, utilities
● Alias: coordinate-mapping
● 0 images

coverageByTranscript (Package: GenomicFeatures) : Compute coverage by transcript (or CDS) of a set of ranges

coverageByTranscript computes the transcript (or CDS) coverage of a set of ranges.

● Data Source: BioConductor
● Keywords: manip
● Alias: coverageByTranscript, pcoverageByTranscript
● 0 images

disjointExons (Package: GenomicFeatures) :

disjointExons extracts the non-overlapping exon parts from a TxDb object or any other supported object.

● Data Source: BioConductor
● Keywords: methods
● Alias: disjointExons, disjointExons,TxDb-method
● 0 images

extractTranscriptSeqs (Package: GenomicFeatures) : Extract transcript (or CDS) sequences from chromosome sequences

extractTranscriptSeqs extracts transcript (or CDS) sequences from an object representing a single chromosome or a collection of chromosomes.

● Data Source: BioConductor
● Keywords: manip
● Alias: extractTranscriptSeqs, extractTranscriptSeqs,ANY-method, extractTranscriptSeqs,DNAString-method
● 0 images

extractUpstreamSeqs (Package: GenomicFeatures) : Extract sequences upstream of a set of genes or transcripts

extractUpstreamSeqs is a generic function for extracting sequences upstream of a supplied set of genes or transcripts.

● Data Source: BioConductor
● Keywords: manip
● Alias: extractUpstreamSeqs, extractUpstreamSeqs,GRangesList-method, extractUpstreamSeqs,GenomicRanges-method, extractUpstreamSeqs,TxDb-method
● 0 images

features (Package: GenomicFeatures) :

Generic function to extract genomic features from a FeatureDb object.

● Data Source: BioConductor
● Keywords:
● Alias: features, features,FeatureDb-method
● 0 images

getPromoterSeq (Package: GenomicFeatures) : Get gene promoter sequences

Extract sequences for the genes or transcripts specified in the query (aGRanges or GRangesList object) from a BSgenome object or an FaFile.

● Data Source: BioConductor
● Keywords: manip, methods
● Alias: getPromoterSeq, getPromoterSeq,GRanges-method, getPromoterSeq,GRangesList-method
● 0 images