caRanges-class {spliceSites} | R Documentation |
"caRanges"
"caRanges"
Objects that contain a centered genomic range and amino acid sequences.
Objects are usually created from objects of class "cdRanges"
by the "translate"
function.
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.
Class "cRanges"
, directly.
signature(x = "caRanges")
: Generic combining for caRanges
objects.
signature(x="caRanges")
: Returns contained sequence (DNAStringSet).
signature(x = "aaGapAligns")
: Returns the first lines of object.
signature(object = "aaGapAligns")
: Returns the last lines of object.
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.
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.
signature(x = "caRanges")
: Exports contained data into "csv" file.
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) Translate into AA sequence ar<-translate(cdr) # E) Truncate and cleave... tra<-truncateSeq(ar) tyc<-trypsinCleave(tra)