ToxicoGx
Analysis of Large-Scale Toxico-Genomic Data

Package index
Search the ToxicoGx package
Vignettes
Functions
127
Source code
54
Man pages
43
Home
/
Bioconductor
/
ToxicoGx
/
ToxicoSet-class: Class to contain Toxico-genomic Data

ToxicoSet-class: Class to contain Toxico-genomic Data
In ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

Description Usage Arguments Value Methods (by generic) Slots Examples

Description

The ToxicoSet (tSet) class was development to contain and organise large ToxicGenomic datasets as well as provide useful tools for interacting with this data. Functions are included for exploring the relationship between survival fraction and gene expression in cultured human and rat tissues during exposure to a wide ranges of compounds. Features include plotting dose and exposure time curves, calculating AUC, fitting linear models and computing sensitivity signatures.

Get the cell line annotations in a ToxicoSet

Set cell line annotations for a ToxicoSet object

Get names of cell lines in a ToxicoSet object

Set the cell line names in a TocicoSet object

Get the date a ToxicoSet object was created

Get the feature names in a ToxicoSet object for the specified molecular data type

Set the feature names in a ToxicoSet object for the specified molecular data type

Set the feature annotations for a specficied molecular data type

Get the molecular profile data associated with the specific molecular data

Set the molecular profile data assciated with the specificied molecular data type

Get an array of the number of pertubration experiments per drug and cell line in a ToxicoSet object

Set the number of perturbation experiments per drug and cell line and molecular data type in a ToxicoSet object

Get the phenotype annotations for cell lines with the specificed molecular data type

Set the phenotype annotations for cell lines with the selected molecular data type.

Get the number of sensitivity experiments per drug and cell line in a ToxicoSet

Set the number of sensitivity experiments per drug and cell line in a ToxicoSet object

Get the annotations for the sensitivity experiments in the ToxicoSet

Set the annotations for sensitivity experiments in this ToxicSet

Get the avilable measurments for sensitivity experiments in a ToxicoSet

Get the data for sensitivty experiments on cell lines in a ToxicoSet

Set the data for sensitivity experiments on cell lines in a ToxicoSet

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
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
## S4 method for signature 'ToxicoSet'
annotation(object)

## S4 replacement method for signature 'ToxicoSet,list'
annotation(object) <- value

## S4 method for signature 'ToxicoSet'
cellInfo(object)

## S4 replacement method for signature 'ToxicoSet,data.frame'
cellInfo(object) <- value

## S4 method for signature 'ToxicoSet'
cellNames(object)

## S4 replacement method for signature 'ToxicoSet,character'
cellNames(object) <- value

## S4 method for signature 'ToxicoSet'
curation(object)

## S4 replacement method for signature 'ToxicoSet,list'
curation(object) <- value

## S4 replacement method for signature 'ToxicoSet'
datasetType(object) <- value

## S4 method for signature 'ToxicoSet'
dateCreated(object)

## S4 method for signature 'ToxicoSet'
datasetType(object)

## S4 method for signature 'ToxicoSet'
drugInfo(object)

## S4 replacement method for signature 'ToxicoSet,data.frame'
drugInfo(object) <- value

## S4 method for signature 'ToxicoSet'
drugNames(object)

## S4 replacement method for signature 'ToxicoSet,character'
drugNames(object) <- value

## S4 method for signature 'ToxicoSet,character'
fNames(object, mDataType)

## S4 replacement method for signature 'ToxicoSet,character,ANY'
fNames(object, mDataType) <- value

## S4 method for signature 'ToxicoSet,character'
featureInfo(object, mDataType)

## S4 replacement method for signature 'ToxicoSet,character,data.frame'
featureInfo(object, mDataType) <- value

## S4 method for signature 'ToxicoSet'
molecularProfiles(object, mDataType, assay)

## S4 replacement method for signature 'ToxicoSet,character,character,matrix'
molecularProfiles(object, mDataType, assay) <- value

## S4 replacement method for signature 'ToxicoSet,character,missing,matrix'
molecularProfiles(object, mDataType, assay) <- value

## S4 method for signature 'ToxicoSet'
molecularProfilesSlot(object)

## S4 replacement method for signature 'ToxicoSet,ANY'
molecularProfilesSlot(object) <- value

## S4 method for signature 'ToxicoSet'
pertNumber(object)

## S4 replacement method for signature 'ToxicoSet,array'
pertNumber(object) <- value

## S4 method for signature 'ToxicoSet,character'
phenoInfo(object, mDataType)

## S4 replacement method for signature 'ToxicoSet,character,data.frame'
phenoInfo(object, mDataType) <- value

## S4 method for signature 'ToxicoSet'
sensNumber(object)

## S4 replacement method for signature 'ToxicoSet,matrix'
sensNumber(object) <- value

## S4 method for signature 'ToxicoSet'
sensitivityInfo(object)

## S4 replacement method for signature 'ToxicoSet,data.frame'
sensitivityInfo(object) <- value

## S4 method for signature 'ToxicoSet'
sensitivityMeasures(object)

## S4 method for signature 'ToxicoSet'
sensitivityProfiles(object)

## S4 replacement method for signature 'ToxicoSet,data.frame'
sensitivityProfiles(object) <- value

## S4 replacement method for signature 'ToxicoSet,matrix'
sensitivityProfiles(object) <- value

## S4 method for signature 'ToxicoSet'
sensitivityRaw(object)

## S4 replacement method for signature 'ToxicoSet,array'
sensitivityRaw(object) <- value

## S4 method for signature 'ToxicoSet'
sensitivitySlot(object)

## S4 replacement method for signature 'ToxicoSet,list'
sensitivitySlot(object, ...) <- value

Arguments

object

A ToxicoSet to extract the raw sensitivity data from

value

A list of new sensitivity slot data for the tSet

mDataType

A character with the type of molecular data to return/update

assay

character Name or index of the assay data to return

...

Allow new parameters to be defined for this generic

Value

An object of the ToxicoSet class

a data.frame with the cell annotations

Updated ToxicoSet

A vector of the cell names used in the ToxicoSet

Updated ToxicoSet

The date the ToxicoSet was created

A character vector of the feature names

Updated ToxicoSet

Updated ToxicoSet

Updated ToxicoSet

A list containing the molecularProfiles from a tSet

A copy of the ToxicoSet with the molecularProfiles slot updated

A 3D array with the number of perturbation experiments per radiation type and cell line, and data type

The updated ToxicoSet

a Dframe with the experiment info

The updated ToxicoSet

A data.frame with the number of sensitivity experiments per drug and cell line

The updated ToxicoSet

a data.frame with the experiment info

Updated ToxicoSet

A character vector of all the available sensitivity measures

a data.frame with the experiment info

Updated ToxicoSet

Methods (by generic)

Slots

annotation

A list of annotation data about the ToxicoSet, including the $name and the session information for how the object was creating, detailing the exact versions of R and all the packages used

molecularProfiles

A list containing SummarizedExperiment type object for holding data for RNA, DNA, SNP and CNV measurements, with associated fData and pData containing the row and column metadata

cell

A data.frame containing the annotations for all the cell lines profiled in the data set, across all data types

drug

A data.frame containg the annotations for all the drugs profiled in the data set, across all data types

sensitivity

A list containing all the data for the sensitivity experiments, including $info, a data.frame containing the experimental info,$raw a 3D array containing raw data, $profiles, a data.frame containing sensitivity profiles statistics, and $n, a data.frame detailing the number of experiments for each cell-drug pair

perturbation

A list containting $n, a data.frame summarizing the available perturbation data,

curation

A list containing mappings for $drug, cell, tissue names used in the data set to universal identifiers used between different ToxicoSet objects

datasetType

A character string of 'sensitivity', 'perturbation', or both detailing what type of data can be found in the ToxicoSet, for proper processing of the data

Examples

 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
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
data(TGGATESsmall)
cellInfo <- cellInfo(TGGATESsmall)

data(TGGATESsmall)
cellInfo(TGGATESsmall) <- cellInfo(TGGATESsmall)

cellNames(TGGATESsmall)

data(TGGATESsmall)
cellNames(TGGATESsmall) <- cellNames(TGGATESsmall)

dateCreated(TGGATESsmall)

data(TGGATESsmall)
datasetType(TGGATESsmall)

fNames(TGGATESsmall, "rna")[seq_len(10)]

data(TGGATESsmall)
cellNames(TGGATESsmall) <- cellNames(TGGATESsmall)

data(TGGATESsmall)
featureInfo <- featureInfo(TGGATESsmall, "rna")[seq_len(10),]

data(TGGATESsmall)
featureInfo(TGGATESsmall, "rna") <- featureInfo(TGGATESsmall, "rna")

data(TGGATESsmall)
TGGATES_mProf <- molecularProfiles(TGGATESsmall, "rna")[seq_len(10),]

molecularProfiles(TGGATESsmall, "rna") <-
  molecularProfiles(TGGATESsmall, "rna")

data(TGGATESsmall)
molecularProfilesSlot(TGGATESsmall)

data(TGGATESsmall)
molecularProfilesSlot(TGGATESsmall) <- molecularProfilesSlot(TGGATESsmall)

pertNumber(TGGATESsmall)

pertNumber(TGGATESsmall) <- pertNumber(TGGATESsmall)

data(TGGATESsmall)
phenoInfo <- phenoInfo(TGGATESsmall, mDataType="rna")

data(TGGATESsmall)
phenoInfo(TGGATESsmall, mDataType="rna") <-
  phenoInfo(TGGATESsmall, mDataType="rna")

sensNumber(TGGATESsmall)

sensNumber(TGGATESsmall) <- sensNumber(TGGATESsmall)

data(TGGATESsmall)
sensInf<- sensitivityInfo(TGGATESsmall)[seq_len(10),]

data(TGGATESsmall)
sensitivityInfo(TGGATESsmall) <- sensitivityInfo(TGGATESsmall)

sensitivityMeasures(TGGATESsmall)

data(TGGATESsmall)
sensProf <- sensitivityProfiles(TGGATESsmall)

sensitivityProfiles(TGGATESsmall) <- sensitivityProfiles(TGGATESsmall)

data(TGGATESsmall)
sensitivitySlot(TGGATESsmall)

data(TGGATESsmall)
sensitivitySlot(TGGATESsmall) <- sensitivitySlot(TGGATESsmall)

ToxicoGx documentation built on Nov. 19, 2020, 2 a.m.

Related to ToxicoSet-class in ToxicoGx...

ToxicoGx index
README.md ToxicoGx: An R Platform for Integrated Toxicogenomics Data Analysis

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close