read_npx_format: Help function to read excel and delimited Olink data files in...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Help function to read excel and delimited Olink data files in R and determine their format, data type and platform.

Description

This function processes Olink software excel or delimited files regardless of data type, platform or format.

Olink software excel files with the extension "xls" or "xlsx" are imported in R by the function read_npx_excel.

Olink software delimited files with suffix "csv" or "txt" are imported in R by the functions read_npx_delim or read_npx_csv.

Files in wide format are subsequently handled by the function read_npx_wide.

Olink software files in wide format always originate from Olink qPCR platforms, and are further processed by the functions read_npx_format_get_platform and read_npx_format_get_quant to determine the data type and Olink platform, respectively.

Usage

read_npx_format(
  file,
  out_df = "arrow",
  long_format = NULL,
  olink_platform = NULL,
  data_type = NULL,
  quiet = FALSE,
  legacy = FALSE
)

Arguments

file	Path to Olink software output file in wide or long format. Expecting file extensions "xls", "xlsx", "csv", or "txt".
out_df	The class of the output dataset. One of "tibble" or "arrow". Defaults to "tibble".
long_format	Boolean marking format of input file. One of TRUE for long format and FALSE for wide format files. Defaults to NULL for auto-detection.
olink_platform	Olink platform used to generate the input file. One of "Target 48", "Flex", "Target 96", "Explore 3072", "Explore HT", "Focus", or "Reveal". Defaults to NULL for auto-detection.
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.
legacy	Boolean to enforce returning a list containing olink_platform, data_type and long_format information together with the dataset. Used only when read_npx_format is called from read_npx_legacy.

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 read_npx_format_read read_npx_format_get_format read_npx_format_get_platform read_npx_format_get_quant read_npx_legacy

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