GenoGAMDataSetList-class {GenoGAM} | R Documentation

## GenoGAMDataSetList

### 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

    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)

- `dim`: Get the dimension of the object

- `length`: The length of the object

- `seqlengths`: The seqlengths of the object

- `seqlevels`: The seqlevels of the object

- `seqlevelsInUse`: The seqlevelsInUse of the object

- `colData`: get colData from the first element of the SummarizedExperiment list

- `rowRanges`: get a list of rowRanges from the GenoGAMDataSetList object

- `assay`: get a list of assays from the GenoGAMDataSetList object

- `assays`: get a list of list of assays from the GenoGAMDataSetList object. Just for completeness, shouldn't be needed.

- `colnames`: get colnames from the first element of the SummarizedExperiment list

- `getIndex`: accessor to the index slot

- `getCountMatrix`: An accessor to the countMatrix slot

- `tileSettings`: The accessor to the list of settings, that were used to generate the tiles.

- `dataRange`: The actual underlying GRanges showing the range of the data.

- `getChromosomes`: A GRanges object representing the chromosomes or chromosome regions on which the model will be computed

- `getTileSize`: The size of the tiles

- `getChunkSize`: The size of the chunks

- `getOverhangSize`: The size of the overhang (on one side)

- `getTileNumber`: The total number of tiles

- `is.HDF5`: A boolean function that is true if object uses HDF5 backend

- `design`: Access to the design slot.

- `design<-`: Replace method of the design slot.

- `sizeFactors`: Access to the sizeFactors slot

- `sizeFactors<-`: Replace method of the sizeFactors slot

- `getChunkSize<-`: Replace method of the chunkSize parameter, that triggers a new computation of the tiles based on the new chunk size.

- `getTileSize<-`: Replace method of the tileSize parameter, that triggers a new computation of the tiles based on the new tile size.

- `getOverhangSize<-`: Replace method of the overhangSize parameter, that triggers a new computation of the tiles based on the new overhang size.

- `getTileNumber<-`: Replace method of the tileNumber parameter, that triggers a new computation of the tiles based on the new number of tiles.

### 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 georg.stricker@in.tum.de

[Package GenoGAM version 2.2.0 Index]