dnaGapSites-class {spliceSites} | R Documentation |
"dnaGapSites"
dnaGapSites contains all data which is stored in objects of class "gapSites"
plus additional DNA sequences in the "seq"
slot.
Objects are usually created from gapSites
via dnaGapSites
.
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.
Class "gapSites"
, directly.
signature(x = "dnaGapSites")
: Returns head of dt.
signature(x = "dnaGapSites")
: Prints seq-logo of stored dna-sequence.
signature(object = "dnaGapSites")
: Prints head of dt.
signature(x = "dnaGapSites")
: Returns an object of class aaalignGaps by translating seq into amino acids.
Wolfgang Kaisers
gapSites
# 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