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