GenoGAM-class: GenoGAM 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 extends the RangedSummarizedExperiment class by adding a couple of more slots to hold hyperparameters and settings. The 'assays' slot holds the basepair fit and standard deviation. Additionally all knot positions and beta coefficients will be stored in the 'smooths' slot in order to be able to make use of the piecewise function that produces the fit. For information on the slots inherited from SummarizedExperiment check the respective class.

The GenoGAM 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
GenoGAM(..., ggd = NULL, fromHDF5 = FALSE, split = FALSE)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

## S4 method for signature 'GenoGAM,GRanges,ANY,ANY'
x[i]

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

split

A logical argument indicating if the model was fitted in a per-chromosome fashion or not. Only needed if fromHDF5 is TRUE.

object, x

For use of S4 methods. The GenoGAM object.

i

A GRanges object (only for subsetting)

Value

An object of the type GenoGAM.

Methods (by generic)

Slots

family

A GenoGAMFamily object

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.

coefs

The coefficients of the knots

knots

The relative knot positions

hdf5

A logical slot indicating if the data is stored in a HDF5 format on hard drive

Author(s)

Georg Stricker [email protected]

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
## 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 Nov. 2, 2018, 6:01 p.m.