Characterization of Alternative Splicing based on Paired-End Reads


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Documentation for package ‘casper’ version 1.1.2

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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"
createDenovoGenome Create an annotatedGenome object that stores information about genes and transcripts
denovoGeneExpr-class Class "denovoGeneExpr"
denovoGenomeExpr-class Class "denovoGenomeExpr"
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.
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.
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"
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"
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
relativeExpr Estimate expression of gene splicing variants de novo.
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"
simMultSamples Simulate paired end reads for multiple samples based on pilot data
simReads Function to simulate paired end reads following given read start and fragment length distributions and gene and variant expressions.
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 "denovoGenomeExpr"
[[-method Class "denovoGeneExpr"