GenoGAMDataSetList-class: GenoGAMDataSetList

Description Usage Arguments Value Methods (by generic) Slots Author(s)

Description

The GenoGAMDataSetList class contains the pre-processed raw data and additional slots that define the input and framework for the model. It extends upon the idea of the GenoGAMDataSet class to make it possible to store genomes and data of size > 2^31 (maximum size of integers in R). Thus the only difference to a GenoGAMDataSet is the arrangement as a list of RangedSummarizedExperiments under the hood. On the surface is does still behave like a GenoGAMDataSet. It is not intended to be used by the user. For more information check the GenoGAMDataSet class documentation.

GenoGAMDataSetList is the constructor function for the GenoGAMDataSetList-class.

Usage

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GenoGAMDataSetList(...)

## S4 method for signature 'GenoGAMDataSetList'
dim(x)

## S4 method for signature 'GenoGAMDataSetList'
length(x)

## S4 method for signature 'GenoGAMDataSetList'
seqlengths(x)

## S4 method for signature 'GenoGAMDataSetList'
seqlevels(x)

## S4 method for signature 'GenoGAMDataSetList'
seqlevelsInUse(x)

## S4 method for signature 'GenoGAMDataSetList'
colData(x, ...)

## S4 method for signature 'GenoGAMDataSetList'
rowRanges(x, ...)

## S4 method for signature 'GenoGAMDataSetList,ANY'
assay(x, i, ...)

## S4 method for signature 'GenoGAMDataSetList'
assays(x, ..., withDimnames = TRUE)

## S4 method for signature 'GenoGAMDataSetList'
colnames(x)

## S4 method for signature 'GenoGAMDataSetList'
getIndex(object)

## S4 method for signature 'GenoGAMDataSetList'
getCountMatrix(object)

## S4 method for signature 'GenoGAMDataSetList'
tileSettings(object)

## S4 method for signature 'GenoGAMDataSetList'
dataRange(object)

## S4 method for signature 'GenoGAMDataSetList'
getChromosomes(object)

## S4 method for signature 'GenoGAMDataSetList'
getTileSize(object)

## S4 method for signature 'GenoGAMDataSetList'
getChunkSize(object)

## S4 method for signature 'GenoGAMDataSetList'
getOverhangSize(object)

## S4 method for signature 'GenoGAMDataSetList'
getTileNumber(object)

## S4 method for signature 'GenoGAMDataSetList'
is.HDF5(object)

## S4 method for signature 'GenoGAMDataSetList'
design(object)

## S4 replacement method for signature 'GenoGAMDataSetList,ANY'
design(object) <- value

## S4 method for signature 'GenoGAMDataSetList'
sizeFactors(object)

## S4 replacement method for signature 'GenoGAMDataSetList,ANY'
sizeFactors(object) <- value

## S4 replacement method for signature 'GenoGAMDataSetList,numeric'
getChunkSize(object) <- value

## S4 replacement method for signature 'GenoGAMDataSetList,numeric'
getTileSize(object) <- value

## S4 replacement method for signature 'GenoGAMDataSetList,numeric'
getOverhangSize(object) <- value

## S4 replacement method for signature 'GenoGAMDataSetList,numeric'
getTileNumber(object) <- value

Arguments

...

The slots and their respective values

withDimnames

For use of S4 methods.

object, x

For use of S4 methods. The GenoGAMDataSetList object.

value, i

For use of S4 methods. The value to be assigned to the slot.

Value

An object of class GenoGAMDataSetList

Methods (by generic)

Slots

settings

The global and local settings that will be used to compute the model.

design

The formula describing how to evaluate the data. See details.

sizeFactors

The normalized values for each sample. A named numeric vector.

index

A GRanges object representing an index of the ranges defined on the genome. Mostly used to store tiles.

data

A list of RangedSummarizedExperiment objects

id

A GRanges object keeping the identifiers assigning the regions to the respective list elements

hdf5

A logical slot indicating if the object should be stored as HDF5

countMatrix

Either a matrix or HDF5Matrix to store the sums of counts of the regions (could also be seen as bins) for later use especially by DESeq2

Author(s)

Georg Stricker [email protected]


GenoGAM documentation built on Dec. 7, 2018, 6 p.m.