caRanges-class {spliceSites} | R Documentation

## Class `"caRanges"`

### Description

`"caRanges"` Objects that contain a centered genomic range and amino acid sequences.

### Objects from the Class

Objects are usually created from objects of class `"cdRanges"` by the `"translate"` function.

### Slots

`dt`:

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

`seq`:

  Object of class `"AAStringSet"`. Contains amino-acid-sequence of ranges described in dt.

### Extends

Class `"cRanges"`, directly.

### Methods

c

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

getSequence

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

head

  `signature(x = "aaGapAligns")`: Returns the first lines of object.

show

  `signature(object = "aaGapAligns")`: Returns the last lines of object.

truncateSeq

  `signature(x="caRanges",rme=TRUE,trunc=42L)`: Truncates contained sequence when character (given by ASCII code in `trunc`). The default (42L) encodes for character '*' which indicates stop-codon.

trypsinCleave

  `signature(x = "caRanges",minLen = 5)`: Performs in silico trypsinization of contained sequence. The sequence fragment which contains the (position depicted) exon-intron boundary is returned. Datasets for which the truncated sequence is shorter than minLen are excluded.

write.files

  `signature(x = "caRanges")`: Exports contained data into "csv" file.

### 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) Translate into AA sequence
    ar<-translate(cdr)
    # E) Truncate and cleave...
    tra<-truncateSeq(ar)
    tyc<-trypsinCleave(tra)

[Package spliceSites version 1.28.0 Index]