annotation {spliceSites} | R Documentation |
gapSites
objectsThe annotate
function takes a gapSites
and a refGenome
object and returns a list
which additionally contains a 'class' attribute 'annotationResult'.
The object is intended as input for the annotation
member
function of class gapSites
.
The annotation
member functions act as writing and reading accessor
for annotation data inside gapSites
objects.
annotate(object, junc)
object |
[gapSites]. Align-gap data for which annotations are provided via overlap. |
junc |
[refJunctions]. Object which provides annotated splice site positions. |
The annotation
reading accessor takes a gapSites
object and returns a annAlignGaps
object.
The annotation
writing accessor takes a gapSites
and a annotationResult
object and copies the contained table
into the annotation
slot of the gapSites
object.
annAlignGaps
Wolfgang Kaisers
# A) Create gapSites object bam <- system.file("extdata", "rna_fem.bam", package="spliceSites") reader <- bamReader(bam[1], idx=TRUE) ga <- alignGapList(reader) bamClose(reader) # B) Read refGenome object ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites") ucj <- loadGenome(ucf) # C) Add annotation data annotation(ga) <- annotate(ga, ucj)