sampleDepth {derfinder} | R Documentation

## Calculate adjustments for library size

### Description

For a given data set calculate the per-sample coverage adjustments. Hector Corrada's group proposed calculating the sum of the coverage for genes below a given sample quantile. In this function, we calculate the sample quantiles of interest by sample, and then the sum of the coverage for bases below or equal to quantiles of interest. The resulting values are transformed log2(x + scalefac) to avoid very large numbers that could potentially affect the stability of the F-statistics calculation. The sample coverage adjustments are then used in makeModels for constructing the null and alternative models.

### Usage

    sampleDepth(collapsedFull, probs = c(0.5, 1), scalefac = 32, ...)

### Arguments

`collapsedFull` | The full coverage data collapsed by sample as produced by collapseFullCoverage.
`probs` | Number(s) between 0 and 1 representing the quantile(s) of interest. For example, 0.5 is the median.
`scalefac` | Number added to the sample coverage adjustments before the log2 transformation.
`...` | Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If `TRUE` basic status updates will be printed along the way. nonzero If `TRUE` only the nonzero counts are used to calculate the library size adjustment. Default: `TRUE`. center If `TRUE` the sample coverage adjustements are centered. In some cases, this could be helpful for interpretation purposes. Default: `FALSE`.

### Value

A matrix (vector of `length(probs) == 1`) with the library size depth adjustments per sample to be used in makeModels. The number of rows corresponds to the number of quantiles used for the sample adjustments.

### Author(s)

Leonardo Collado-Torres

### References

Paulson, J. N., Stine, O. C., Bravo, H. C. & Pop, M. Differential abundance analysis for microbial marker-gene surveys. Nat. Methods (2013). doi:10.1038/nmeth.2658

### See Also

collapseFullCoverage, makeModels

### Examples

    ## Collapse the coverage information
    collapsedFull <- collapseFullCoverage(list(genomeData$coverage),
        verbose=TRUE)

    ## Calculate library size adjustments
    sampleDepths <- sampleDepth(collapsedFull, probs=c(0.5, 1), verbose=TRUE)
    sampleDepths

[Package derfinder version 1.14.0 Index]