NormalyzerDataset: Represents raw input data together with basic annotation...

Description Usage Arguments Value Slots

View source: R/NormalyzerDataset.R

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

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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.


NormalyzerDE documentation built on Nov. 8, 2020, 8:22 p.m.