K562.r1l1               Toy RNA-seq data from RGASP project.
annotatedGenome-class   Class "annotatedGenome"
asymmetryCheck          Plot asymmetry coefficients for the observed
                        data and compare to those expected under
                        Normality.
calcDenovo              Estimate expression of gene splicing variants
                        de novo.
calcExp                 Estimate expression of a known set of gene
                        splicing variants.
denovoExpr              Estimate expression for de novo splicing
                        variants.
denovoGeneExpr-class    Class "denovoGeneExpr"
denovoGenomeExpr-class
                        Class "denovoGenomeExpr"
distrsGSE37704          Estimated read start and insert size
                        distributions from MiSeq data in GEO dataset
                        GSE37704.
genePlot                Plot exon structure for each transcript of a
                        given gene.
getDistrs               Compute fragment start and fragment length
                        distributions
getIsland               getIsland returns the island id associated to a
                        given entrez or transcript id in an
                        annotatedGenome object. getChr indicates the
                        chromosome for a given Entrez, transcript or
                        island id.
getNreads               Get total number of paths in each island from a
                        pathCounts object.
getReads                getReads returns the reads stored in a
                        'procBam' object.
getRoc                  Operating characteristics of differential
                        expression analysis
hg19DB                  Subset of human genome (UCSC hg19 version)
mergeBatches            Merge two ExpressionSet objects by doing
                        quantile normalization and computing partial
                        residuals (i.e. substracting group mean
                        expression in each batch). As currently
                        implemented the method is only valid for
                        balanced designs, e.g. each batch has the same
                        number of samples per group.
mergeExp                Merge splicing variant expression from multiple
                        samples
modelPrior              Set prior distribution on expressed splicing
                        variants.
modelPriorAS-class      Class "modelPriorAS"
pathCounts              Compute exon path counts
pathCounts-class        Class "pathCounts"
plot                    Plot estimated read start and fragment length
                        distributions.
plotExpr                Plot inferred gene structure and expression.
plotPriorAS             Plot prior distribution on set of expressed
                        variants (i.e. the model space).
probNonEquiv            'probNonEquiv' performs a Bayesian hypothesis
                        test for equivalence between group means.  It
                        returns the posterior probability that
                        |mu1-mu2|>logfc. 'pvalTreat' is a wrapper to
                        'treat' in package 'limma', which returns
                        P-values for the same hypothesis test.
procBam                 Process BAM object
procBam-class           Class "procBam"
procGenome              Create an annotatedGenome object that stores
                        information about genes and transcripts
qqnormGenomeWide        Genome-wide qq-normal and qq-gamma plots
quantileNorm            Apply quantile normalization
relexprByGene           Compute relative expressions within each gene
rmShortInserts          Remove reads with short insert sizes from
                        imported BAM files.
simMAE                  Simulate Mean Absolute Error (MAE) in
                        estimating isoform expression under various
                        experimental settings.
simMAEcheck             Model checking for One Sample Problems.
simMultSamples          Simulate paired end reads for multiple future
                        samples based on pilot data, and obtain their
                        expression estimates via casper
simReads                Function to simulate paired end reads following
                        given read start and fragment length
                        distributions and gene and variant expressions.
simulatedSamples-class
                        Class "simulatedSamples"
splitGenomeByLength     Split an annotatedGenome object into subsets
                        according to gene length
subsetGenome            subsetGenome subsets an object of class
                        annotatedGenome for a set of island IDs or
                        chromosome names.
transcripts             Extracts transcript information (exon start and
                        ends) from an 'annotatedGenome' object, either
                        for all transcripts or only those corresponding
                        to a given island or transcript.
txLength                ~~ Methods for Function 'txLength' in Package
                        'casper' ~~
wrapDenovo              Run all necessary steps to get expression
                        estimates from multiple bam files with the
                        casper pipeline.
wrapKnown               Run all necessary steps to get expression
                        estimates from multiple bam files with the
                        casper pipeline.
