getVariantPercentages {R453Plus1Toolbox} | R Documentation

## Variant coverage

### Description

This function computes the coverage for each variant (in forward and/or reverse direction) for all samples. The coverage is defined as the percentual amount of reads that cover a variant.

### Usage

    getVariantPercentages(object, direction="both")

### Arguments

`object` | An instance of class `AVASet-class` or `MapperSet-class`.
`direction` | A character indicating the direction ("forward", "reverse" or "both").

### Details

If the direction was set to "both", the percentages are computed over the sum of both directions. Otherwise it is computed only over the occurences in one direction (forward or reverse). The occurences can be accesses via `assayData`.

### Value

`getVariantPercentages` returns a data frame with all percentages/frequencies for all samples.

### Author(s)

Christoph Bartenhagen

### See Also

`setVariantFilter`.

### Examples

    # load a (filtered) AVA dataset containing 6 samples, 4 amplicons and 4 variants
    data(avaSetFiltered)
    avaSetFiltered

    # both directions
    getVariantPercentages(avaSetFiltered, direction="both")
    # this is equivalent to
    (assayData(avaSetFiltered)[[1]] + assayData(avaSetFiltered)[[3]]) / (assayData(avaSetFiltered)[[2]] + assayData(avaSetFiltered)[[4]])

    # forward direction only
    getVariantPercentages(avaSetFiltered, direction="forward")
    # this is equivalent to
    assayData(avaSetFiltered)[[1]] / assayData(avaSetFiltered)[[2]]

    # reverse direction only
    getVariantPercentages(avaSetFiltered, direction="reverse")
    # this is equivalent to
    assayData(avaSetFiltered)[[3]] / assayData(avaSetFiltered)[[4]]

[Package R453Plus1Toolbox version 1.40.0 Index]