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

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)