GenoGAMList-class: GenoGAMList class
In gstricker/fastGenoGAM: A GAM based framework for analysis of ChIP-Seq data

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

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.

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)

`...`	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.

An object of the type GenoGAM.

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

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

Georg Stricker georg.stricker@in.tum.de

## 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)