Class "dnaGapSites"

Description

dnaGapSites contains all data which is stored in objects of class "gapSites" plus additional DNA sequences in the "seq" slot.

Objects from the Class

Objects are usually created from gapSites via dnaGapSites.

Slots

seq:

"DNAStringSet". Contains DNA sequence.

nAligns:

code"numeric". Contains total number of aligns.

nAlignGaps:

"numeric". Contains total number of align gaps.

dt:

code"data.frame". Contains data on gap-sites.

Extends

Class "gapSites", directly.

Methods

head

signature(x = "dnaGapSites"): Returns head of dt.

seqlogo

signature(x = "dnaGapSites"): Prints seq-logo of stored dna-sequence.

show

signature(object = "dnaGapSites"): Prints head of dt.

translate

signature(x = "dnaGapSites"): Returns an object of class aaalignGaps by translating seq into amino acids.

Author(s)

Wolfgang Kaisers

See Also

gapSites

Examples

# A) Read gapSites
bam<-system.file("extdata", "rna_fem.bam", package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
# B) Load DNA sequence
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
# C 1) Add DNA
dga<-dnaGapSites(ga,dna_small)
dga
# C 2) Calculate codon positions
lrj<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='+')
lrc<-lrCodons(lrj,frame=1,strand='+')
# D) Add DNA sequence and translate
lrd<-dnaGapSites(lrc,dna_small)
lra<-translate(lrd)
lra