cdRanges-class: Class '"cdRanges"'

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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)

spliceSites documentation built on May 6, 2019, 3:05 a.m.