correctBins {QDNAseq} | R Documentation

## Correct binned read counts for GC content and mappability

### Description

Correct binned read counts for GC content and mappability.

### Usage

    correctBins(object, fit=NULL, method="ratio", adjustIncompletes=TRUE, ...)

### Arguments

`object` | An `QDNAseqReadCounts` object with `counts` data.
`fit` | An optional matrix of values to use for the correction. If NULL (default), assay data `fit` from object is used. If it is missing, it is generated with a call to `estimateCorrection`().
`method` | A character(1) string speficying the correction method. `ratio` (default) divides `counts` with `fit`. `median` calculates the median `fit`, and defines the correction for bins with GC content `gc` and mappability `map` as `median(fit) - fit(gc,map)`, which is added to `counts`. Method `none` leaves `counts` untouched.
`adjustIncompletes` | A boolean(1) specifying whether `counts` for bins with uncharacterized nucleotides (N's) in their reference genome sequence should be adjusted by dividing them with the percentage of characterized (A, C, G, T) nucleotides. Defaults to `TRUE`.
`...` | Additional arguments passed to `estimateCorrection`().

### Value

Returns a `QDNAseqCopyNumbers` object with assay data element `copynumber`.

### Author(s)

Ilari Scheinin

### See Also

Internally, `loess` is used to fit the regression model.

### Examples

    data(LGG150)
    readCounts <- LGG150
    readCountsFiltered <- applyFilters(readCounts)
    readCountsFiltered <- estimateCorrection(readCountsFiltered)
    copyNumbers <- correctBins(readCountsFiltered)

[Package QDNAseq version 1.16.0 Index]