IntSpan method is changed to count reads that span the whole
intron precisely. Previous these were counted separayted for 5' end and
3' end of the introns.
repeatsTableToFilter is ignored for IntSpana nd ExSkip as
the skipped regions of the reads (denoted by N or sometimes D in the
CIGAR of bam/sam file ) are taken into count for these benchmarks (not
the mapped regions which are dentoed with Ms in the cigar).
strandSpecific is a new parameter added to interest() and interest.sequential(). It indicates that
IntEREst is now strand-aware. All analysis can be run whilst taking into account (or ignoring) the strand specificity of the sequencing reads.
referencePrepare can create references (with collapsed exons) that does not ignore the strand information.
GenomicFiles::reduceByYield function is now used instead of
BiocParallel::bpiterat for improved efficiency and readability.
This relates to how analysis related to different pieces of the alignment
data is distributed over the parallel cores and the results are sumarized.
In interest() and and interest.sequential()
The oredr of the results of the different methods in the result
matrix is corrected. Correct running of analyses using multiple
methods with a single command is now possible.
method parameter in interest() and interest.sequential() functions now support
"ExSkip". For each exon, the fucntions can now count the number of reads that skip over the exons.
limitRanges parameter in interest() and interest.sequential() functions allow for targetted analysis. It only loads reads that map to the defined coordinates.
Replacing class( x ) == "foo" with is( x , "foo") .
applyOverlap() Apply a function on counts of a
SummarizedExperiment basd on the overlaps of its genome
coordinates to with another SummarizedExperiment.
referencePrepare() stopped from modifying chromosome
names.I doesn't add "chr" to the beginning of chromosome names.
interest() and interest.sequential() functions
support the possibility to define other parameter settings of
BamFile() function of Rsamtools package e.g.
"qnamePrefixEnd" and "qnameSuffixStart".
annotateU12() can return the PWM match scores (if
requested). The hybrid AT-AG and GT-AC U12 types can be set to be
ignored. The introns/exons coordinates can be filtered according
to their map to another set of coordinates.
referencePrepare() just gives warning and continue
without annotating gene names (when annotateGeneIds=TRUE
parameter is set) if annotating with gene names is not
possible.
interest() used to return Error if single end mapped
reads did not existed at all (despite being requetsed). This has
been corrected.
buildSsTypePwms() function supports the possibility
to select begin and end point of splice sites sequences from which
PWMs are built. It also supports the possibility to paste splice
sites to build PWM.
interest.sequential() and interest():
corrections to their object output option.
annotateU12() modified to work correctly with the new
changes in Biostrings package.
buildSsTypePwms() corrected and modified to better
suit data for all species from SpliceRack and U12DB.
interest() and interest.sequential() functions
now support "IntSpan" method, allows counting intron-
spanning reads.
psi() function is added. It calculates Psi values.
annotateU12() fucntion supports DNAStringSet objects
as its refGenome input.
Improved vignette document.
eBayesInterest() removed.
interest.sequential() and interest():
corrections to their object output option.
annotateU12() modified to work correctly with the new
changes in Biostrings package.