GenoGAMSettings-class {GenoGAM} | R Documentation

## GenoGAMSettings

### Description

This class is designed to store settings for the computation of the GenoGAM package

### Details

Center can have three values: TRUE, FALSE, NULL. TRUE will trigger the center function, FALSE will trigger the use of the entire fragment. NULL should be used in case a custom process function is used.

### Slots

`center`

  A logical or NULL value to specify if the raw data should be centered, i.e. only the midpoint of the fragment will be used to represent its coverage. See details.

`chromosomeList`

  A character vector of chromosomes to be used. NULL for all chromosomes.

`bamParams`

  An object of class ScanBamParam. See ?Rsamtools::ScanBamParam.

`parallel`

  A parallel backend of the respective class. See BiocParalell for the options

`processFunction`

  A custom function on how to process raw data. Not used if center is TRUE/FALSE.

`optimMethod`

  The optiomisation method to be used in cross validation.

`optimControl`

  Settings for the optim() function.

### Author(s)

Georg Stricker georg.stricker@in.tum.de

[Package GenoGAM version 1.8.0 Index]