cdRanges-class {spliceSites} | R Documentation |
"cdRanges"
"cdRanges"
Objects that contain centered Ranges (exon-intron junctions) and dna-sequences.
Objects are usually created from "cRanges"
with the function "dnaRanges"
.
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.
Class "cRanges"
, directly.
signature(x = "cdRanges")
: Generic combining for cdRanges
objects.
signature(x="cdRanges")
: Returns contained sequence (DNAStringSet).
signature(x = "cdRanges")
: Prints first items from object.
signature(.Object = "cdRanges")
: Create an instance of class using new
.
signature(x = "cdRanges")
: Show a seqlogo of contained sequences
signature(x = "cdRanges")
: Translates dna-sequence into amino-acid-sequence. Returns an object of class "caRanges"
.
Wolfgang Kaisers
cRanges
# 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)