NormalyzerDataset {NormalyzerDE} | R Documentation

## Represents raw input data together with basic annotation information

### Description

Takes a job name, a data matrix, a design matrix as well as specification of the group and sample columns in the design matrix. Provides the basic representation of a dataset in the NormalyzerDE normalization part.

### Usage

    NormalyzerDataset(jobName, designMatrix, rawData, annotationData,
      sampleNameCol, groupNameCol, tinyRunThres = 50, quiet = FALSE)

    NormalyzerDataset(jobName, designMatrix, rawData, annotationData,
      sampleNameCol, groupNameCol, tinyRunThres = 50, quiet = FALSE)

### Arguments

`jobName` | Name of the NormalyzerDE processing run
`designMatrix` | Matrix containing sample conditions
`rawData` | Matrix containing raw input data
`annotationData` | Matrix containing annotation information for each input feature. Is expected to contain the same number of rows as the data but can contain any number of features
`sampleNameCol` | Name of column in design matrix containing sample information
`groupNameCol` | Name of column in design matrix containing condition information
`tinyRunThres` | If fewer features than this is present in the input a limited run will be performed to avoid some steps requiring a more extensive number of features.
`quiet` | If set to TRUE no information messages will be printed

### Value

nds Generated NormalyzerDataset instance

### Slots

`jobName`

  Name of the job represented by the dataset.

`rawData`

  Matrix with raw values.

`sampleNameCol`

  Name column for sample.

`groupNameCol`

  Name column for groups.

`designMatrix`

  Data frame containing design.

`sampleNames`

  Vector containing sample names.

`filterrawdata`

  Reduced raw data matrix where low abundance rows are removed

`sampleReplicateGroups`

  Vector with sample replicate information

`samplesGroupsWithReplicates`

  Vector with replicated sample replicate information

`annotationValues`

  Annotation part of original dataframe.

`retentionTimes`

  Vector of retention time values.

`singleReplicateRun`

  Conditional whether run is single replicate.

[Package NormalyzerDE version 1.4.0 Index]