calcExp {casper} | R Documentation

## Estimate expression of a known set of gene splicing variants.

### Description

Estimate expression of gene splicing variants, assuming that the set of variants is known. When `rpkm` is set to `TRUE`, fragments per kilobase per million are returned. Otherwise relative expression estimates are returned.

### Usage

    calcExp(distrs, genomeDB, pc, readLength, islandid, rpkm=TRUE, priorq=2,
    priorqGeneExpr=2, citype="none", niter=10^3, burnin=100, mc.cores=1, verbose=FALSE)

### Arguments

`distrs` | List of fragment distributions as generated by the `getDistrs` function
`genomeDB` | `knownGenome` object containing annotated genome, as returned by the `procGenome` function.
`pc` | Named vector of exon path counts as returned by `pathCounts`
`readLength` | Read length in bp, e.g. in a paired-end experiment where 75bp are sequenced on each end one would set `readLength=75`.
`islandid` | Name of the gene island to be analyzed. If not specified, all gene islands are analyzed.
`rpkm` | Set to `FALSE` to return relative expression levels, i.e. the proportion of reads generated from each variant per gene. These proportions add up to 1 for each gene. Set to `TRUE` to return fragments per kilobase per million (RPKM).
`priorq` | Parameter of the prior distribution on the proportion of reads coming from each variant. The prior is Dirichlet with prior sample size for each variant equal to priorq. We recommend `priorq=2` for estimation, as it pools the estimated expression away from 0 and 1 and returned lower estimation errors than `priorq=1` in our simulated experiments.
`priorqGeneExpr` | Parameter for prior distribution on overall gene expression. Defaults to 2, which ensures non-zero estimates for all genes
`citype` | Set to `"none"` to return no credibility intervals. Set to `"asymp"` to return approximate 95% CIs (obtained via the delta method). Set to `"exact"` to obtain exact CIs via Monte Carlo simulation. Options `"asymp"` and especially `"exact"` can increase the computation time substantially.
`niter` | Number of Monte Carlo iterations. Only used when `citype=="exact"`.
`burnin` | Number of burnin Monte Carlo iterations. Only used when `citype=="exact"`.
`mc.cores` | Number of processors to be used for parallel computation. Can only be used if the package `multicore` is available for your system.
`verbose` | Set to `TRUE` to display progress information.

### Value

Expression set with expression estimates. `featureNames` identify each transcript via RefSeq ids, and the `featureData` contains further information. If `citype` was set to a value other than `"none"`, the `featureData` also contains the 95% credibility intervals (i.e. intervals that contain the true parameter value with 95% posterior probability).

### Author(s)

Camille Stephan-Otto Attolini, Manuel Kroiss, 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

`relexprByGene`

### Examples

    data(K562.r1l1)
    data(hg19DB)

    #Pre-process
    bam0 <- rmShortInserts(K562.r1l1, isizeMin=100)
    pbam0 <- procBam(bam0)
    head(getReads(pbam0))

    #Estimate distributions, get path counts
    distrs <- getDistrs(hg19DB,bam=bam0,readLength=75)
    pc <- pathCounts(pbam0, DB=hg19DB)

    #Get estimates
    eset <- calcExp(distrs=distrs, genomeDB=hg19DB, pc=pc, readLength=75, rpkm=FALSE)
    head(exprs(eset))
    head(fData(eset))

    #Re-normalize relative expression to add up to 1 within gene_id rather
    # than island_id
    eset <- relexprByGene(eset)

    #Add fake sample by permuting and combine
    eset2 <- eset[sample(1:nrow(eset),replace=FALSE),]
    sampleNames(eset2) <- '2' #must have a different name
    esetall <- mergeExp(eset,eset2)

    #After merge samples are correctly matched
    head(exprs(esetall))
    head(fData(esetall))

[Package casper version 2.14.0 Index]