The addHbond methods add HBond scores to gapSites and cdRanges objects. HBond scores provide a measure for the capability of a 5' splice-site to form H-bonds with the U1 snRNA. The function requires at least 3 exon nucleotides and 8 intron nucleotides. The first two intron nucleotides are expected to be 'GT' (for other values the returned score will be 0). The routine equally accepts upper and lower case characters.
addMaxEnt
(Package: spliceSites) :
addMaxEnt: Extract subset of data contained in given range given object.
addMaxEnt adds new columns to object data which contain MaxEnt-Score derived values. mxe_ps5 contains score5 values for left align-gap (exon-intron) boundary (i.e. assumed to reside on '+'-strand. mxe_ps3 contains score3 (maxent) values for right align-gap (intron-exon) boundary (i.e. assumed to reside on '+'-strand). mxe_ms5 contains score5 values for right align-gap (exon-intron) boundary on reverseComplement transformed sequence (i.e. assumed to reside on '-'-strand). mxe_ms3 contains score3 values for left align-gap (intron-exon) boundary on reverseComplement transformed sequence (i.e. assumed to reside on '-'-strand). From these values, s3strand, s5strand and meStrand are derived: s3strand is '+' when mxe_ps5 >= mxe_ms5 and '-' otherwise; s3strand is '+' when mxe_ps3 >= mxe_ms3 and '-' otherwise. meStrand equals s5strand when s5strand=s3strand and '*' otherwise. The function setMeStrand copies existing meStrand values into strand column (and throws an error when meStrand does not exist).
alt_X_ranks
(Package: spliceSites) :
alt_left_ranks and alt_right_ranks functions: Identification of
alt_X_ranks covers the functions alt_left_ranks and alt_right_ranks. Both functions identify alternative splice-sites. alt_left_ranks finds sites which share the same rstart value (on the same seqid). alt_right_ranks finds sites which share the same lend value (on the same seqid). alt_ranks combines the results of both functions together wich seqid, lend and rstart values in one table.
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.
Reads featureData from incoming Expression set which should contain range data on embedding exons for gap-sites. The annotate function then overlaps the ranges with given annotation data. The result of overlapping is written into a AnnotatedDataFrame.
The 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.
providing 
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