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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" |