annGapSites-class: Class '"annGapSites"'

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

Description

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.

Details

plot_diff plots tabled distance between inner gap-site border and annotated exon-intron boundaries.

Objects from the Class

Objects can be created by calls of the form annotation on gapSites objects.

Slots

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).

Extends

Class "gapSites", directly.

Methods

as.data.frame

signature(x = "annGapSites"): Returns the contained data.

Author(s)

Wolfgang Kaisers

Examples

# 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)

spliceSites documentation built on May 6, 2019, 3:05 a.m.