annGapSites-class {spliceSites} | R Documentation |
"annGapSites"
Contains data from align gaps together with annotation data
(and optional data about alternative splice positions).
Objects of this clasa are returned from the annotation
member function
for class gapSites
.
plot_diff
plots tabled distance between inner gap-site border and
annotated exon-intron boundaries.
Objects can be created by calls of the form annotation
on gapSites
objects.
nAligns
:Object of class "numeric"
Total number of aligns.
nAlignGaps
:Object of class "numeric"
Total number of gapped aligns.
dt
:"data.frame"
. Contains gap-positions,
annotation data and optional alternative position data.
annotation
:"data.frame"
.
Contains annotation data.
profile
:"data.frame"
.
Contains descriptive data for source probes (BAM-files).
Class "gapSites"
, directly.
signature(x = "annGapSites")
:
Returns the contained data.
Wolfgang Kaisers
# A) Read gapSites from BAM bam <- system.file("extdata", "rna_fem.bam", package="spliceSites") reader <- bamReader(bam, idx=TRUE) ga <- alignGapList(reader) bamClose(reader) # B) Load annotation data ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites") ucj <- loadGenome(ucf) # C) Add Annotation annotation(ga) <- annotate(ga, ucj) # D) Retrieve annotation aga <- annotation(ga) aga # D) plot_diff aga <- annotation(ga) plot_diff(aga)