gapSites: Creating 'gapSites' and 'dnaGapSites' objects.

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

Description

gapSites creates objects of class gapSites from scratch. dnaGapSites creates objects of class dnaGapSites from gapSites objects.

Usage

gapSites(seqid=factor(),lstart=integer(),lend=integer(),
                    rstart=integer(),rend=integer(),gaplen,strand,
                    nr_aligns=1,nAligns=sum(nr_aligns),
                    nAlignGaps=sum(nr_aligns),nProbes=1)

Arguments

seqid	Character.Identifies reference sequence.
lstart	Coordinates for start of left range.
lend	Coordinates for end of left range. Usually exon-intron boundary.
rstart	Coordinates for start of right range. Usually exon-intron boundary.
rend	Coordinates for end of right range.
gaplen	Length of enclosed gap. Should equal rstart-lend-1.
strand	+ or - or * (for unknown). Default: '*'.
nr_aligns	Number of gapped aligns which have the same exon-intron boundaries (lend and rstart)
nAligns	Total number of aligns for probeset.
nAlignGaps	Total lnumber of gapped aligns for probeset.
nProbes	Numeric. Number of probes in which this gapped position is present.

Details

The intended way to create a gapSites object is to use the alignGapList function which in turn calls the (rbamtools) bamGapList function. When a BAM file almoust exclusively contains gapped aligns which sometimes are multiply gapped, possibly the 'nAlignGaps' value is greater than the 'nAligns'. When reading BAM files which contain the complete date of an alignment, usually the 'nAlignGaps' value is about $1/3$ of the 'nAligns' value.

Value

An object of class 'gapSites'.

Author(s)

Wolfgang Kaisers

Examples

# A) Construct source data from scratch
seqid<-c("chr1","chr1","chr2","chr2","chr2")
lstart<-c(900, 1900,900 ,900, 1900)
lend  <-c(1000,2000,1000,1000,2000)
rstart<-c(1100,2100,1100,1200,2100)
rend  <-c(1200,2200,1200,1300,2200)
nr_aligns<-c(10,20,30,40,10)

# B) Construct gapSites object
ga<-gapSites(seqid,lstart,lend,rstart,rend,nr_aligns=nr_aligns)
ga

# C) Use gapSites accessors
seqid(ga)
lend(ga)
rstart(ga)
strand(ga)
gptm(ga)
rpmg(ga)
nAligns(ga)
nAlignGaps(ga)

# D) Create 
bam<-system.file("extdata", "rna_fem.bam", package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
ga
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
dga<-dnaGapSites(ga,dna_small)

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