GenoGAMList-class {GenoGAM} | R Documentation

## GenoGAMList class

### Description

This is the class the holds the complete model as well all hyperparameters and settings that were used to fit it. It is basically identical to the GenoGAM class, except for the data being inside a list of RangedSummarizedExperiment objects.

The GenoGAMList constructor, not designed to be actually used, by the user. Rather to be a point of reference and documentation for slots and how to access them.

### Usage

    GenoGAMList(..., ggd = NULL, fromHDF5 = FALSE)

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

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

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

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

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

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

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

    ## S4 method for signature 'GenoGAMList'
    getSettings(object)

    ## S4 method for signature 'GenoGAMList'
    getFamily(object)

    ## S4 method for signature 'GenoGAMList'
    colData(x)

    ## S4 method for signature 'GenoGAMList'
    getParams(object)

    ## S4 method for signature 'GenoGAMList'
    getCoefs(object)

    ## S4 method for signature 'GenoGAMList'
    getKnots(object)

    ## S4 method for signature 'GenoGAMList,missing'
    assay(x, i)

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

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

    ## S4 method for signature 'GenoGAMList'
    fits(object)

    ## S4 method for signature 'GenoGAMList'
    se(object)

    ## S4 method for signature 'GenoGAMList'
    pvalue(object)

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

    ## S4 method for signature 'GenoGAMList'
    dimnames(x)

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

### Arguments

`...` | Slots of the GenoGAM class. See the slot description.
`ggd` | The initial GenoGAMDataSet object. Only needed if fromHDF5 is TRUE.
`fromHDF5` | A convenience argument to create a GenoGAM object from the already computed fits that are stored as HDF5 files
`object, x` | For use of S4 methods. The GenoGAMList object.
`i` | A GRanges object (only for subsetting)
`withDimnames` | For use of S4 methods. The GenoGAMList object.

### Value

An object of the type GenoGAM.

### 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

- `design`: An accessor to the design slot

- `sizeFactors`: An accessor to the sizeFactors slot

- `getSettings`: An accessor to the settings slot

- `getFamily`: An accessor to the family slot

- `colData`: An accessor to the factorialDesign slot.

- `getParams`: An accessor to the params slot

- `getCoefs`: An accessor to the coefs slot

- `getKnots`: An accessor to the knots slot

- `assay`: The accessor to the fits and standard errors

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

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

- `fits`: An accessor to the fits

- `se`: An accessor to the standard errors

- `pvalue`: An accessor to the pvalues

- `colnames`: column names of GenoGAMList

- `dimnames`: The names of the dimensions of GenoGAMList

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

### Slots

`family`

  The name of the distribution family used

`design`

  The formula of the model

`sizeFactors`

  The offset used in the model.

`factorialDesign`

  The factorial design used. The same as colData in the GenoGAMDataSet

`params`

  All hyperparameters used to fit the data. The parameters estimated by cross validation can also be found here. But the parameters used in cross validation are in the settings slot.

`settings`

  A GenoGAMSettings object representing the global settings that were used to compute the model.

`data`

  A list of RangedSummarizedExperiment that holds the actual data

`id`

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

`coefs`

  The coefficients of the knots

`knots`

  The relative knot positions

### Author(s)

Georg Stricker georg.stricker@in.tum.de

### Examples

    ## creating test GenoGAM object
    gg <- makeTestGenoGAM()
    gg

    ## using accessors
    design(gg)
    sizeFactors(gg)
    getSettings(gg)
    getFamily(gg)
    colData(gg)
    getParams(gg)
    getCoefs(gg)
    getKnots(gg)
    rowRanges(gg)
    assay(gg)
    assays(gg)
    fits(gg)
    se(gg)

[Package GenoGAM version 2.10.0 Index]