compData-class {compcodeR} | R Documentation

## Class compData

### Description

The `compData` class is used to store information about the experiment, such as the count matrix, sample and variable annotations, information regarding the generation of the data and results from applying a differential expression analysis to the data.

### Slots

`count.matrix`:

  The read count matrix, with genes as rows and samples as columns. Class `matrix`

`sample.annotations`:

  A data frame containing sample annotation information for all samples in the data set. Must contain at least a column named `condition`, encoding the division of the samples into two classes. The row names should be the same as the column names of `count.matrix`. Class `data.frame`

`info.parameters`:

  A list of parameters detailing the simulation process used to generate the data. Must contain at least two entries, named `dataset` (an informative name for the data set/simulation setting) and `uID` (a unique ID for the specific data set instance). Class `list`

`filtering`:

  A character string detailing the filtering process that has been applied to the data. Class `character`

`variable.annotations`:

  Contains information regarding the variables, such as the differential expression status, the true mean, dispersion and effect sizes. If present, the row names should be the same as those of `count.matrix`. Class `data.frame`

`analysis.date`:

  (If a differential expression analysis has been performed and the results are included in the `compData` object). Gives the date when the differential expression analysis was performed. Class `character`

`package.version`:

  (If a differential expression analysis has been performed and the results are included in the `compData` object). Gives the version numbers of the package(s) used for the differential expression analysis. Class `character`

`method.names`:

  (If a differential expression analysis has been performed and the results are included in the `compData` object). A list, containing the name of the method used for the differential expression analysis. The list should have two entries: `full.name` and `short.name`, where the `full.name` is the full (potentially long) name identifying the method, and `short.name` may be an abbreviation. Class `list`

`code`:

  (If a differential expression analysis has been performed and the results are included in the `compData` object). A character string containing the code that was used to run the differential expression analysis. The code should be in R markdown format. Class `character`

`result.table`:

  (If a differential expression analysis has been performed and the results are included in the `compData` object). Contains the results of the differential expression analysis, in the form of a data frame with one row per gene. Must contain at least one column named `score`, where a higher value corresponds to 'more strongly differentially expressed genes'. Class `data.frame`

### Methods

count.matrix

  `signature(x="compData")`

count.matrix<-

  `signature(x="compData",value="matrix")`: Get or set the count matrix in a `compData` object. `value` should be a numeric matrix.

sample.annotations

  `signature(x="compData")`

sample.annotations<-

  `signature(x="compData",value="data.frame")`: Get or set the sample annotations data frame in a `compData` object. `value` should be a data frame with at least a column named 'condition'.

info.parameters

  `signature(x="compData")`

info.parameters<-

  `signature(x="compData",value="list")`: Get or set the list with info parameters in a `compData` object. `value` should be a list with at least elements named 'dataset' and 'uID'.

filtering

  `signature(x="compData")`

filtering<-

  `signature(x="compData",value="character")`: Get or set the information about the filtering in a `compData` object. `value` should be a character string describing the filtering that has been performed.

variable.annotations

  `signature(x="compData")`

variable.annotations<-

  `signature(x="compData",value="data.frame")`: Get or set the variable annotations data frame in a `compData` object. `value` should be a data frame.

analysis.date

  `signature(x="compData")`

analysis.date<-

  `signature(x="compData",value="character")`: Get or set the analysis date in a `compData` object. `value` should be a character string describing when the differential expression analysis of the data was performed.

package.version

  `signature(x="compData")`

package.version<-

  `signature(x="compData",value="character")`: Get or set the information about the package version in a `compData` object. `value` should be a character string detailing which packages and versions were used to perform the differential expression analysis of the data.

method.names

  `signature(x="compData")`

method.names<-

  `signature(x="compData",value="list")`: Get or set the method names in a `compData` object. `value` should be a list with slots `full.name` and `short.name`, giving the full name and an abbreviation for the method that was used to perform the analysis of the data.

code

  `signature(x="compData")`

code<-

  `signature(x="compData",value="character")`: Get or set the code slot in a `compData` object. `value` should be a character string in R markdown format, giving the code that was run to obtain the results from the differential expression analysis.

result.table

  `signature(x="compData")`

result.table<-

  `signature(x="compData",value="data.frame")`: Get or set the result table in a `compData` object. `value` should be a data frame with one row per gene, and at least a column named 'score'.

### Construction

An object of the class `compData` can be constructed using the `compData` function.

### Author(s)

Charlotte Soneson

[Package compcodeR version 1.22.0 Index]