# Characterization of Alternative Splicing based on Paired-End Reads

## Documentation for package ‘casper’ version 2.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E G H K L M N P Q R S T V W misc

## -- A --

annotatedGenome | Class "annotatedGenome"
annotatedGenome-class | Class "annotatedGenome"
as.list-method | Class "denovoGenomeExpr"
asymmetryCheck | Plot asymmetry coefficients for the observed data and compare to those expected under Normality.
asymmetryCheck-method | Plot asymmetry coefficients for the observed data and compare to those expected under Normality.

## -- C --

calcDenovo | Estimate expression of gene splicing variants de novo.
calcExp | Estimate expression of a known set of gene splicing variants.
casperDesign | Simulate paired end reads for multiple future samples based on pilot data, and obtain their expression estimates via casper
coef-method | Class "modelPriorAS"
coef-method | Class "simulatedSamples"
createDenovoGenome | Create an annotatedGenome object that stores information about genes and transcripts

## -- D --

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.

## -- E --

exprs-method | Class "simulatedSamples"

## -- G --

genePlot | Plot exon structure for each transcript of a given gene.
genePlot-method | Plot exon structure for each transcript of a given gene.
genePlot-methods | Plot exon structure for each transcript of a given gene.
getChr | 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.
getChr-method | 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.
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.
getIsland-method | 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.
getNreads-method | Get total number of paths in each island from a pathCounts object.
getReads | getReads returns the reads stored in a 'procBam' object.
getReads-method | getReads returns the reads stored in a 'procBam' object.
getRoc | Operating characteristics of differential expression analysis
getRoc-method | Operating characteristics of differential expression analysis

## -- H --

hg19DB | Subset of human genome (UCSC hg19 version)

## -- K --

K562.r1l1 | Toy RNA-seq data from RGASP project.

## -- L --

lines | Plot estimated read start and fragment length distributions.
lines-method | Plot estimated read start and fragment length distributions.

## -- M --

matchTranscripts | 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.
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.
mergeBatches-method | 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"

## -- N --

names-method | Class "denovoGeneExpr"

## -- P --

pathCounts | Compute exon path counts
pathCounts-class | Class "pathCounts"
pathCounts-method | Compute exon path counts
plot | Plot estimated read start and fragment length distributions.
plot-method | Plot estimated read start and fragment length distributions.
plotExpr | Plot inferred gene structure and expression.
plotExpr-method | Plot inferred gene structure and expression.
plotExpr-methods | Plot inferred gene structure and expression.
plotPriorAS | Plot prior distribution on set of expressed variants (i.e. the model space).
plotPriorAS-method | Plot prior distribution on set of expressed variants (i.e. the model space).
plotPriorAS-methods | Plot prior distribution on set of expressed variants (i.e. the model space).
posprob | Class "denovoGeneExpr"
posprob-method | Class "denovoGeneExpr"
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.
probNonEquiv-method | '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"
procBam-method | Process BAM object
procGenome | Create an annotatedGenome object that stores information about genes and transcripts
procGenome-method | Create an annotatedGenome object that stores information about genes and transcripts
pvalTreat | '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.
pvalTreat-method | '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.

## -- Q --

qqgammaGenomeWide | Genome-wide qq-normal and qq-gamma plots
qqgammaGenomeWide-method | Genome-wide qq-normal and qq-gamma plots
qqnormGenomeWide | Genome-wide qq-normal and qq-gamma plots
qqnormGenomeWide-method | Genome-wide qq-normal and qq-gamma plots
quantileNorm | Apply quantile normalization
quantileNorm-method | Apply quantile normalization

## -- R --

relexprByGene | Compute relative expressions within each gene
rmShortInserts | Remove reads with short insert sizes from imported BAM files.

## -- S --

show-method | Class "annotatedGenome"
show-method | Class "denovoGenomeExpr"
show-method | Class "denovoGeneExpr"
show-method | Class "modelPriorAS"
show-method | Class "pathCounts"
show-method | Class "procBam"
show-method | Class "simulatedSamples"
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.
subsetGenome-method | subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names.
subsetGenome-methods | subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names.

## -- T --

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.
transcripts-method | 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' ~~
txLength-method | ~~ Methods for Function 'txLength' in Package 'casper' ~~
txLength-methods | ~~ Methods for Function 'txLength' in Package 'casper' ~~

## -- V --

variants | Class "denovoGeneExpr"
variants-method | Class "denovoGeneExpr"
variants<- | Class "denovoGeneExpr"
variants<--method | Class "denovoGeneExpr"

## -- W --

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.

## -- misc --

[-method | Class "denovoGenomeExpr"
[-method | Class "denovoGeneExpr"
[-method | Class "modelPriorAS"
[-method | Class "simulatedSamples"
[[-method | Class "denovoGenomeExpr"
[[-method | Class "denovoGeneExpr"