setupRawDataObject {NormalyzerDE} | R Documentation |
Prepare SummarizedExperiment object for raw data to be normalized containing data, design and annotation information
setupRawDataObject(dataPath, designPath, inputFormat = "default", zeroToNA = FALSE, sampleColName = "sample", groupColName = "group")
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 |
experimentObj SummarizedExperiment object loaded with the data
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)