cRanges-class: Class '"cRanges"': Centered ranges.

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

Description

"cRanges" Objects that contain centered genomic ranges. The center position marks a prominent position inside the range, generally an exon-intron junction. Position values represent the 0-based position of last exon nucleotide.

Objects from the Class

Objects can be created by calls of the form new("cRanges", seqnames, start, end, width, strand, position, id).

Slots

dt:

Object of class "data.frame". The data.frame contains the columns id, seqnames, start, end, width, strand and position. Each row contains data for one centered range.

Methods

as.data.frame

signature(x = "cRanges"): Returns a copy of the contained data inside a data.frame object.

c

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

count

signature(x = "cRanges"): Returns the number of contained ranges (number of rows).

dim

signature(x = "cRanges"): Returns the dim of the contained data.frame.

dnaRanges

signature(x = "cRanges", dnaset="DNAStringSet",useStrand="logical",removeUnknownStrand=logical): Takes a cRanges object and a DNAStringSet (a reference sequence) and adds the appropriate DNA sequence to the genomic ranges. Returns a cdRanges object.

end

signature(x = "cRanges"): Returns end column of data.

head

signature(x = "cRanges",n="numeric",digits="numeric"): Returns first n (default: n=6) lines of contained data.frame.

id

signature(x = "cRanges"): Returns id column from contained data.frame.

initialize

signature(.Object = "cRanges"): Generic class initialisation method.

lCodons

signature(x = "cRanges",frame="numeric", keepStrand="logical"): Returns cRanges object which represents ranges truncated to codon size. When 'keepStrand' is set to FALSE, strand is set to '+'. The intention is that appended DNA sequences which then can be translated into amino acids.

rCodons

signature(x = "cRanges",frame="numeric", keepStrand="logical"): Returns cRanges object which represents ranges truncated to codon size. When 'keepStrand' is set to FALSE, strand is set to '+'. The intention is that appended DNA sequences which then can be translated into amino acids.

seqid

signature(x = "cRanges"): Returns vector with seqid's.

show

signature(object = "cRanges"): Generic print function.

sortTable

signature(x="cRanges"): Sort contained tables by seqid,lend and rstart.

start

signature(x = "cRanges"): Returns start column from contained data.frame.

strand

signature(x = "cRanges"): Returns strand column from contained data.frame.

width

signature(x = "cRanges"): Returns width of contained ranges (=end-start+1).

Author(s)

Wolfgang Kaisers

See Also

gapRanges

Examples

# A) Create cRanges object from scratch
sq<-factor(c(1,1,2,2,3,3),labels=c("chr1","chr2","chr3"))
st<-c(100,200,100,300,100,400)
en<-c(120,210,110,310,110,410)
pos<-c(2,3,4,5,6,7)
cr<-new("cRanges",seqid=sq,start=st,end=en,position=pos)
cr
seqid(cr)
start(cr)
end(cr)
width(cr)
strand(cr)
id(cr)
lCodons(cr,frame=1,keepStrand=TRUE)
lCodons(cr,frame=1,keepStrand=FALSE)
lCodons(cr,frame=2,keepStrand=TRUE)
rCodons(cr,frame=1,keepStrand=FALSE)
# + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #
# B) Intended way to create a cRanges object from BAM data
bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)
ga
lj<-lJunc(ga,featlen=3,gaplen=6,strand='+')
lj
# C) ...
table(strand(lj))

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.