Skip to contents

Read and Process Olink NPX Data File

read_olink.Rd

This function reads and processes an Olink NPX file in long format. It supports `.csv`, `.xls`, `.xlsx`, `.txt`, `.zip`, and `.parquet` formats, using Olink's own OlinkAnalyze::read_NPX() function, and returns a metaboprep object or a list of matrices and metadata frames for further analysis.

Usage

read_olink(filepath, return_Metaboprep = FALSE)

Arguments

filepath

A string specifying the path to the Olink NPX file.

return_Metaboprep

logical, if TRUE (default) return a Metaboprep object, if FALSE return a list.

Value

Metaboprep object or a named list with the following elements:

data

A matrix of NPX values with `SampleID` as rows and `OlinkID` as columns, containing only sample data.

samples

A `data.frame` containing metadata for samples.

features

A `data.frame` containing feature-level metadata for samples.

controls

A matrix of NPX values for control samples.

control_metadata

A `data.frame` containing metadata for control samples.

Details

The function checks whether the input data is in long format by verifying the presence of duplicate `SampleID` values. It also accommodates two variants of Olink files:

  • Files that include a `Sample_Type` column with values `"SAMPLE"` and `"CONTROL"`.

  • Files that use the `SampleID` column to label control samples (e.g., entries containing `"CONTROL"`).

If neither format is detected, the function stops with an error indicating that the data is likely not from Olink.

Examples

if (FALSE) { # \dontrun{
  filepath <- system.file("extdata", "example_olink_data.txt", package = "metaboprep")
  olink_data <- read_olink(filepath)
} # }