read_npx_legacy: Olink legacy function for reading NPX or absolute...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Olink legacy function for reading NPX or absolute quantification data in wide format into R from qPCR Olink products.

Description

This implementation of read_NPX does not cover the latest versions of Olink files in wide format. Specifically, it supports:

• Target 96 output files in wide format (T96 reports only NPX) with the bottom matrix containing one of the following combinations of rows:

  • Missing Data freq. and LOD. # nolint: line_length_linter

  • Missing Data freq., LOD, and Normalization. # nolint: line_length_linter

• Target 48 output files in wide format NPX with the bottom matrix containing the following rows: Missing Data freq., Normalization, and LOD. # nolint: line_length_linter

• Target 48 output files in wide format absolute Quantification with the bottom matrix containing the following rows: Assay warning, LLOQ, Lowest quantifiable level, Missing Data freq., Normalization, Plate_LOD, and ULOQ. # nolint: line_length_linter

This function would accept data exported in wide format from Olink NPX Signature 1.7.1 or earlier, or NPX Manager.

Usage

read_npx_legacy(
  file,
  out_df = "tibble",
  olink_platform = NULL,
  data_type = NULL,
  quiet = TRUE
)

Arguments

file	Path to Olink software output file in wide format. Expected one of file extensions "xls", "xlsx", "csv", or "txt".
out_df	The class of the output dataset. One of "tibble" or "arrow". Defaults to "tibble".
olink_platform	Olink platform used to generate the input file. One of NULL (default) for auto-detection, "Flex", "Focus", "Target 48", or "Target 96".
data_type	Quantification method of the input data. One of "Ct", "NPX", or "Quantified". Defaults to NULL for auto-detection.
quiet	Boolean to print a confirmation message when reading the input file. Applies to excel or delimited input only. TRUE skips printing the message, and FALSE otherwise.

Value

Dataset, "tibble" or "ArrowObject", with Olink data in long format.

Author(s)

Klev Diamanti Kathleen Nevola Pascal Pucholt Christoffer Cambronero Boxi Zhang Olof Mansson Marianne Sandin

See Also

read_npx_format_read read_npx_format_get_format read_npx_format_get_platform read_npx_format_get_quant

OlinkAnalyze documentation built on June 24, 2026, 1:06 a.m.