GenomicTiles-class


This class is designed to represent the entire genome (or a subset of
it) and any additional data associated with the samples or positions.
It extends the RangedSummarizedExperiment class and adds two additional
index slots to keep track of the data. The main change compared to
RangedSummarizedExperiment is the use of a GPos (basepair level) instead of
GRanges (ranges level) object as rowRanges and the use of two GRanges objects
as indices. The GPos object allows to store raw instead of summarized data
in the assays. Because of this the size of genomic data can increase
tremendously. Thus the GenomicTiles class automatically divides the data
in (overlapping) tiles, making any operation on this data easy executable
in parallel.


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

GenomicTiles-class function

 <dl>
<dt><code>index</code></dt><dd>A GRanges object that stores the tiles ranges and their index
in the genome space. That is, ranges are the positions on the genome.</dd> <dt><code>coordinates</code></dt><dd>A GRanges object that stores the tiles ranges and their index
in the DataFrame space. That is ranges are the row positions in the DataFrame.</dd> </dl>

Slots

This class is designed to represent the entire genome (or a subset of
it) and any additional data associated with the samples or positions.
It extends the RangedSummarizedExperiment class and adds two additional
index slots to keep track of the data. The main change compared to
RangedSummarizedExperiment is the use of a GPos (basepair level) instead of
GRanges (ranges level) object as rowRanges and the use of two GRanges objects
as indices. The GPos object allows to store raw instead of summarized data
in the assays. Because of this the size of genomic data can increase
tremendously. Thus the GenomicTiles class automatically divides the data
in (overlapping) tiles, making any operation on this data easy executable
in parallel.

GenomicTiles-class: GenomicTiles class

Description

Arguments

Slots

Details