estimateCorrection {QDNAseq} | R Documentation

## Estimate correction to read counts for GC content and mappability

### Description

Estimate correction to read counts for GC content and mappability.

### Usage

    estimateCorrection(object, span=0.65, family="symmetric", adjustIncompletes=TRUE,
      maxIter=1, cutoff=4, variables=c("gc", "mappability"), ...)

### Arguments

`object` | An `QDNAseqReadCounts` object with `counts` data.
`span` | For `loess`, the parameter alpha which controls the degree of smoothing.
`family` | For `loess`, if "gaussian" fitting is by least-squares, and if "symmetric" a re-descending M estimator is used with Tukey's biweight function.
`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`.
`maxIter` | An integer(1) specifying the maximum number of iterations to perform, default is 1. If larger, after the first loess fit, bins with median residuals larger than `cutoff` are removed, and the fitting repeated until the list of bins to use stabilizes or after `maxIter` iterations.
`cutoff` | A numeric(1) specifying the number of standard deviations (as estimated with `madDiff`) the cutoff for removal of bins with median residuals larger than the cutoff. Not used if `maxIter=1` (default).
`variables` | A character vector specifying which variables to include in the correction. Can be `c("gc", "mappability")` (the default), `"gc"`, or `"mappability"`.
`...` | Additional arguments passed to `loess`.

### Value

Returns a `QDNAseqReadCounts` object with the assay data element `fit` added.

### Parallel processing

This function uses future to calculate the QDNAseq model across samples in parallel.

### 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)

[Package QDNAseq version 1.30.0 Index]