setupRawDataObject: Prepare SummarizedExperiment object for raw data to be...

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

Prepare SummarizedExperiment object for raw data to be normalized containing data, design and annotation information

Description

Prepare SummarizedExperiment object for raw data to be normalized containing data, design and annotation information

Usage

setupRawDataObject(
  dataPath,
  designPath,
  inputFormat = "default",
  zeroToNA = FALSE,
  sampleColName = "sample",
  groupColName = "group"
)

Arguments

dataPath	File path to data matrix.
designPath	File path to design matrix.
inputFormat	Type of matrix for data, can be either 'default', 'proteios', 'maxquantprot' or 'maxquantpep'
zeroToNA	If TRUE zeroes in the data is automatically converted to NA values
sampleColName	Column name for column containing sample names
groupColName	Column name for column containing condition levels

Value

experimentObj SummarizedExperiment object loaded with the data

Examples

data_path <- system.file(package="NormalyzerDE", "extdata", "tiny_data.tsv")
design_path <- system.file(package="NormalyzerDE", "extdata", "tiny_design.tsv")
df <- setupRawDataObject(data_path, design_path)

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