dnaGapSites-class {spliceSites} | R Documentation

## Class `"dnaGapSites"`

### Description

dnaGapSites contains all data which is stored in objects of class `"gapSites"` plus additional DNA sequences in the `"seq"` slot.

### Objects from the Class

Objects are usually created from `gapSites` via `dnaGapSites`.

### Slots

`seq`:

  `"DNAStringSet"`. Contains DNA sequence.

`nAligns`:

  code"numeric". Contains total number of aligns.

`nAlignGaps`:

  `"numeric"`. Contains total number of align gaps.

`dt`:

  code"data.frame". Contains data on gap-sites.

### Extends

Class `"gapSites"`, directly.

### Methods

head

  `signature(x = "dnaGapSites")`: Returns head of dt.

seqlogo

  `signature(x = "dnaGapSites")`: Prints seq-logo of stored dna-sequence.

show

  `signature(object = "dnaGapSites")`: Prints head of dt.

translate

  `signature(x = "dnaGapSites")`: Returns an object of class aaalignGaps by translating seq into amino acids.

### Author(s)

Wolfgang Kaisers

### See Also

gapSites

### Examples

    # A) Read gapSites
    bam<-system.file("extdata", "rna_fem.bam", package="spliceSites")
    reader<-bamReader(bam,idx=TRUE)
    ga<-alignGapList(reader)
    # B) Load DNA sequence
    dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
    load(dnafile)
    # C 1) Add DNA
    dga<-dnaGapSites(ga,dna_small)
    dga
    # C 2) Calculate codon positions
    lrj<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='+')
    lrc<-lrCodons(lrj,frame=1,strand='+')
    # D) Add DNA sequence and translate
    lrd<-dnaGapSites(lrc,dna_small)
    lra<-translate(lrd)
    lra

[Package spliceSites version 1.28.0 Index]