aaGapSites-class {spliceSites} | R Documentation |
"aaGapSites"
Contains gapAligns data and a AAStringSet.
Objects can be created by calls of the form new("aaGapSites", ...)
.
seq
:"AAStringSet"
:
Contains amino acid sequences.
nAligns
:"numeric"
:
Contains total number of aligns.
nAlignGaps
:"numeric"
:
Contains total number of align gaps.
dt
:"data.frame"
:
Contains data for all gap sites.
Class "gapSites"
, directly.
signature(x = "aaGapSites")
:
Returns the first lines of object.
signature(object = "aaGapSites")
:
Returns the last lines of object.
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.
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.
signature(x = "caRanges")
:
Exports contained data into "csv" file.
Wolfgang Kaisers
# A) Read gap-sites from BAM-file bam <- system.file("extdata", "rna_fem.bam", package="spliceSites") reader <- bamReader(bam, idx=TRUE) ga <- alignGapList(reader) bamClose(reader) # B) Load reference dna dnafile <- system.file("extdata", "dna_small.RData", package="spliceSites") load(dnafile) # C) Calculate cross junctional ranges lrj <- lrJunc(ga, lfeatlen=6, rfeatlen=6, strand='+') lr1 <- lrCodons(lrj, frame=1, strand='+') lr2 <- lrCodons(lrj, frame=2, strand='+') lr3 <- lrCodons(lrj, frame=3, strand='+') lr <- c(lr1, lr2, lr3) # D) Add DNA-sequence lrd <- dnaGapSites(lr, dna_small) # E) Translate DNA to amino acid lra <- translate(lrd)