caRanges-class: Class '"caRanges"'

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

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)

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