cdRanges-class {spliceSites} | R Documentation

## Class `"cdRanges"`

### Description

`"cdRanges"` Objects that contain centered Ranges (exon-intron junctions) and dna-sequences.

### Objects from the Class

Objects are usually created from `"cRanges"` with the function `"dnaRanges"`.

### Slots

`dt`:

  Object of class `"data.frame"`. Contains the columns `"seqid"`,`"start"`,`"end"`,`"strand"`,`"position"`,`"id"`,`"frame"`.

`seq`:

  Object of class `"DNAStringSet"`. Contains the dna-sequence of ranges described in dt.

### Extends

Class `"cRanges"`, directly.

### Methods

c

  `signature(x = "cdRanges")`: Generic combining for `cdRanges` objects.

getSequence

  `signature(x="cdRanges")`: Returns contained sequence (DNAStringSet).

head

  `signature(x = "cdRanges")`: Prints first items from object.

initialize

  `signature(.Object = "cdRanges")`: Create an instance of class using `new`.

seqlogo

  `signature(x = "cdRanges")`: Show a seqlogo of contained sequences

translate

  `signature(x = "cdRanges")`: Translates dna-sequence into amino-acid-sequence. Returns an object of class `"caRanges"`.

### Author(s)

Wolfgang Kaisers

### See Also

cRanges

### Examples

    # A) Read gapSites object
    bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
    reader<-bamReader(bam,idx=TRUE)
    ga<-alignGapList(reader)
    bamClose(reader)
    ga
    # B) Create cRanges object
    lj<-lJunc(ga,featlen=21,gaplen=21,strand='+')
    ljc<-lCodons(lj,frame=1,keepStrand=TRUE)
    dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
    load(dnafile)
    # C) Add DNA sequence
    cdr<-dnaRanges(ljc,dna_small)
    # D) seqLogo ...
    seqlogo(cdr)

[Package spliceSites version 1.28.0 Index]