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

In ComputationalProteomics/NormalyzerDE: Evaluation of normalization methods and calculation of differential expression analysis statistics

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.

ComputationalProteomics/NormalyzerDE documentation built on Sept. 18, 2023, 9:15 p.m.