R: Gene copy numbers with confidence intervals through...

runBootstrap {CNOGpro} | R Documentation

## Gene copy numbers with confidence intervals through bootstrapping

### Description

For each genetic element in the gene table of a `CNOGpro` object, sample repeatedly from the read observations associated with that gene while replacing the observations.

### Usage

    runBootstrap(experiment, replicates = 1000, quantiles = c(0.025, 0.975))

### Arguments

`experiment` | An object of class `CNOGpro`
`replicates` | The (integer) number of resampling experiments per genetic element. (That is, the number of bootstrap samples.)
`quantiles` | The quantiles of the distribution of mean copy numbers for which the mean is returned. (Given as c(lower, upper))

### Details

Implements the theory that since the read counts from each genetic element come from a (overdispersed) Poisson distribution with rate parameter lambda (=mean), this lambda can be inferred by simply taking the mean of the observations from that genetic element. A confidence interval is then constructed around the mean by random resampling with replacement. For each replicate and genetic element, the same number of samples is taken as there are read count observations associated with that particular genetic element. The observations of means are then sorted and the given lower and upper quantiles are returned.

### Value

An object of class `CNOGpro`, with proposed copy number (floating point) and the associated confidence interval for each genetic element in the table of genes.

### Author(s)

Ola Brynildsrud

### Examples

    data(carsonella)
    carsonella_normalized <- normalizeGC(carsonella)
    carsonella_bootstrapped <- runBootstrap(carsonella, replicates=500)
    printCNOGpro(carsonella_bootstrapped)

[Package CNOGpro version 1.1 Index]