GenoGAMSettings-class


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


This package allows statistical analysis of genome-wide
data with smooth functions using generalized additive models
based on the implementation from the R-package 'mgcv'. It
provides methods for the statistical analysis of ChIP-Seq data
including inference of protein occupancy, and pointwise and
region-wise differential analysis. Estimation of dispersion and
smoothing parameters is performed by cross-validation. Scaling
of generalized additive model fitting to whole chromosomes is
achieved by parallelization over overlapping genomic intervals.

Georg Stricker

GenoGAM

A GAM based framework for analysis of ChIP-Seq data

GenoGAMSettings-class function

 <dl>
<dt><code>center</code></dt><dd>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.</dd> <dt><code>chromosomeList</code></dt><dd>A character vector of chromosomes to be used.
NULL for all chromosomes.</dd> <dt><code>bamParams</code></dt><dd>An object of class ScanBamParam.
See ?Rsamtools::ScanBamParam.</dd> <dt><code>parallel</code></dt><dd>A parallel backend of the respective class. See
BiocParalell for the options</dd> <dt><code>processFunction</code></dt><dd>A custom function on how to process raw data. Not
used if center is TRUE/FALSE.</dd> <dt><code>optimMethod</code></dt><dd>The optiomisation method to be used in cross validation.</dd> <dt><code>optimControl</code></dt><dd>Settings for the optim() function.</dd> </dl>

Slots

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

GenoGAMSettings-class: GenoGAMSettings

Description

Arguments

Slots

Details