GenoGAMList-class: GenoGAMList class

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

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

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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)

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 [email protected]

Examples

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## 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)

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