setupRawDataObject {NormalyzerDE} | R Documentation

## 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)

[Package NormalyzerDE version 1.2.0 Index]