wrapDenovo {casper} | R Documentation

## Run all necessary steps to get expression estimates from multiple bam files with the casper pipeline.

### Description

Function to analyze bam files to generate an ExpressionSet with expression estimates for all samples, read start and fragment length distributions, path counts and optinally processed reads.

### Usage

    wrapDenovo(bamFile, output_wrapKnown, knownGenomeDB, targetGenomeDB, readLength,
      rpkm=TRUE, keep.multihits=TRUE, searchMethod="submodels",
      exactMarginal=TRUE,  integrateMethod = "plugin", maxExons=40,
      islandid, chroms=NULL, keep.pbam=FALSE,  keepPbamInMemory=FALSE,
      niter=10^3, priorq=3, priorqGeneExpr=2,
      mc.cores.int=1, mc.cores=1, verbose=TRUE, seed=1)

### Arguments

`bamFile` | Names of bam files with the sample to analyze. These must sorted and indexed, and the index must be in the same directory.
`output_wrapKnown` | Optional argument containing the output of an earlier call to `wrapKnown`. If provided, path counts, read start and insert size distributions are loaded from this output rather than being re-computed. Better leave this argument missing unless you know what you're doing.
`knownGenomeDB` | `annotatedGenome` object with known isoforms, e.g. from UCSC or GENCODE annotations. Used to set the prior probability that any given isoform is expressed. See help(calcDenovo) for details.
`targetGenomeDB` | `annotatedGenome` object with isoforms we wish to quantify. By default these are the same as in `knownGenomeDB`, but more typically `targetGenomeDB` is imported from a .gtf file produced by some isoform prediction software.
`readLength` | Read length in bp, e.g. in a paired-end experiment where 75bp are sequenced on each end one would set `readLength=75`.
`rpkm` | Set to `TRUE` to return reads per kilobase per million (RPKM), `FALSE` for relative expression levels. Important, relative expression adds up to 1 within gene island, NOT within gene. To get relative expressions within gene run `relexprByGene` afterwards. See help(wrapKnown).
`keep.multihits` | Set to `FALSE` to discard reads aligned to multiple positions.
`searchMethod` | Method used to perform the model search. `"allmodels"` enumerates all possible models (warning: this is not feasible for genes with >5 exons). `"rwmcmc"` uses a random-walk MCMC scheme to focus on models with high posterior probability. `"submodels"` considers that some isoforms in `targetGenomeDB` may not be expressed, but does not search for new variants. `"auto"` uses `"allmodels"` for genes with up to 5 exons and `"rwmcmc"` for longer genes. See help("calcDenovo").
`exactMarginal` | Set to `FALSE` to estimate posterior model probabilities as the proportion of MCMC visits. Set to `TRUE` to use the integrated likelihoods (default). See details.
`integrateMethod` | Method to compute integrated likelihoods. The default (`'plugin'`) evaluates likelihood*prior at the posterior mode and is the faster option. Set `'Laplace'` for Laplace approximations and `'IS'` for Importance Sampling. The latter increases computation cost very substantially.
`maxExons` | Prior probabilities of isoform expression are estimated for genes with 1 up to `maxExons` exons separately, for genes with more than `maxExons` exons a combined estimate is used. See `help("modelPrior")`
`islandid` | Names of the gene island to be analyzed. If missing all gene islands are analyzed
`chroms` | Names of the chromosomes to be analyzed. If missing all chromosomes are analyzed.
`keep.pbam` | Set to `TRUE` to save processed bam object, as returned by `procBam`. This object can require substantial memory during execution and disk storage upon saving and is not needed for a default analysis.
`keepPbamInMemory` | Set to `TRUE` to keep processed bam objects in memory to speed up some computations.
`niter` | Number of MCMC iterations in the model search algorithm.
`priorq` | Parameter of the Dirichlet prior for the proportion of reads coming from each variant. We recommend `priorq=3` as this defines a non-local prior that penalizes falsely predicted isoforms.
`priorqGeneExpr` | Parameter of the Dirichlet prior distribution on overall gene expression. Defaults to 2 to ensure non-zero estimates.
`mc.cores` | Number of cores to use in expression estimation.
`mc.cores.int` | Number of cores to use when loading bam files. Be careful as this is a memory intensive step.
`verbose` | Set to `TRUE` to display progress information.
`seed` | Set seed of random number generator.

### Details

The function executes the functions `procBam`, `getDistrs`, `pathCounts` `calcDenovo` and `denovoExpr` and formats the output nicely. Running `wrapDenovo` is much more efficient in cpu speed and memory usage than running these functions separately.

When `rpkm` is false the function returns the estimated proportion of reads arising from each isoform within a gene island. See the details in `help("wrapKnown")` for more information on this.

### Value

`denovoGenomeDB` | `annotatedGenome` that contains the isoforms in `targetGenomeDB` plus any new isoforms predicted by casper

.

`exp` | Object of class `ExpressionSet` containing Bayesian model averaging expression estimates. See the fData for the posterior probability that each isoform is expressed.
`distr` | Object of class `readDistrs`
`pbam` | List of objects of class `procBam` with one element per chromosome

### Author(s)

Miranda Stobbe, David Rossell

### References

Rossell D, Stephan-Otto Attolini C, Kroiss M, Stocker A. Quantifying Alternative Splicing from Paired-End RNA-sequencing data. Annals of Applied Statistics, 8(1):309-330.

### See Also

`calcDenovo`, `wrapKnown`, `relexprByGene`

### Examples

    ## not run
    ## Known isoforms
    ##  library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    ##  hg19DB <- procGenome(TxDb.Hsapiens.UCSC.hg19.knownGene), genome='hg19')

    ## gtf with known & de novo predictions
    ##  mygtf <- import('hg19_denovo.gtf')
    ##  hg19denovoDB <- procGenome(mygtf, genome='hg19')

    ## bamFile="/path_to_bam/sorted.bam"
    ##  ans <- wrapDenovo(bamFile=bamFile, targetGenomeDB=hg19denovoDB, knownGenomeDB=hg19DB, readLength=101)

    ## Estimated expression via BMA
    ##  head(exprs(ans[['exp']]))

    ## Posterior probability that each isoform is expressed
    ##  head(fData(ans[['exp']]))

[Package casper version 2.20.0 Index]