# Characterization of Alternative Splicing based on Paired-End Reads

## Documentation for package ‘casper’ version 1.9.0

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

## Help Pages

annotatedGenome | Class "annotatedGenome"
annotatedGenome-class | Class "annotatedGenome"
as.list-method | Class "denovoGenomeExpr"
calcDenovo | Estimate expression of gene splicing variants de novo.
calcExp | Estimate expression of a known set of gene splicing variants.
coef-method | Class "modelPriorAS"
coef-method | Class "simulatedSamples"
createDenovoGenome | Create an annotatedGenome object that stores information about genes and transcripts
denovoExpr | Estimate expression for de novo splicing variants.
denovoGeneExpr-class | Class "denovoGeneExpr"
denovoGenomeExpr-class | Class "denovoGenomeExpr"
exprs-method | Class "simulatedSamples"
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
hg19DB | Subset of human genome (UCSC hg19 version)
K562.r1l1 | Toy RNA-seq data from RGASP project.
lines | Plot estimated read start and fragment length distributions.
lines-method | Plot estimated read start and fragment length distributions.
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"
names-method | Class "denovoGeneExpr"
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 | Posterior probability that differences between group means are greater than a given threshold, i.e. that groups are non-equivalent by a biologically meaningful amount.
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
quantileNorm | Apply quantile normalization
quantileNorm-method | Apply quantile normalization
relativeExpr | Estimate expression of gene splicing variants de novo.
relexprByGene | Compute relative expressions within each gene
rmShortInserts | Remove reads with short insert sizes from imported BAM files.
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"
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.
transcripts | Returns all transcripts associated to a given island or entrez id stored in an annotatedGenome object.
transcripts-method | Returns all transcripts associated to a given island or entrez id stored in an annotatedGenome object.
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' ~~
variants | Class "denovoGeneExpr"
variants-method | Class "denovoGeneExpr"
variants<- | Class "denovoGeneExpr"
variants<--method | Class "denovoGeneExpr"
wrapKnown | Run all necessary steps to analyze a bam file with the casper pipeline.
[-method | Class "denovoGenomeExpr"
[-method | Class "denovoGeneExpr"
[-method | Class "modelPriorAS"
[-method | Class "simulatedSamples"
[[-method | Class "denovoGenomeExpr"
[[-method | Class "denovoGeneExpr"