olink_normalization_product_format: Formatting the output of olink_normalization_product for...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Formatting the output of olink_normalization_product for seamless use with downstream Olink Analyze functions.

Description

Replaces the NPX values of the non-reference project by the Median Centered or QS Normalized NPX, according to the Bridging Recommendation. Edits the BridgingRecommendation column to indicate whether an assay is NotBridgeable, NotOverlapping, MedianCentering, or QuantileSmoothing bridged. Replaces OlinkID by the concatenation of the Explore HT and Explore 3072 OlinkIDs to record the OlinkIDs from both projects for bridgeable assays. Assays that are NotBridgeable or NotOverlapping retain their original non-reference OlinkIDs and NPX values. Replaces SampleID with the concatenation of SampleID and Project to make unique sample IDs for downstream analysis. Removes internal and external controls. Removes MedianCenteredNPX, QSNormalizedNPX, OlinkID_E3072 columns.

Usage

olink_normalization_product_format(
  bridged_df,
  df1,
  df1_project_nr,
  df2,
  df2_project_nr,
  reference_project
)

Arguments

bridged_df	A "tibble" of Olink data in long format resulting from the olink_normalization_product function.
df1	First dataset to be used for normalization, pre-normalization. Must match df1 used in olink_normalization product bridging.
df1_project_nr	Project name of first dataset. Must match name used in olink_normalization product bridging.
df2	Second dataset to be used for normalization, pre-normalization. Must match df2 used in olink_normalization product bridging.
df2_project_nr	Project name of second dataset. Must match name used in olink_normalization product bridging.
reference_project	Project name of reference project. Must match name used in olink_normalization product bridging and be one of df1_project_nr or df2_project_nr.

Value

A "tibble" of Olink data in long format containing both input datasets with the bridged NPX quantifications, with the above modifications.

Author(s)

Danai G. Topouza

Examples

# Bridge samples
bridge_samples <- intersect(
  x = unique(OlinkAnalyze:::data_ht_small$SampleID),
  y = unique(OlinkAnalyze:::data_3k_small$SampleID)
) |>
  (\(x) x[!grepl("CONTROL", x)])()

# Run olink_normalization_product
npx_br_data <- olink_normalization(
df1 = OlinkAnalyze:::data_ht_small,
df2 = OlinkAnalyze:::data_3k_small,
overlapping_samples_df1 = bridge_samples,
df1_project_nr = "Explore HT",
df2_project_nr = "Explore 3072",
reference_project = "Explore HT")

# Format output
npx_br_data_format <- OlinkAnalyze:::olink_normalization_product_format(
bridged_df = npx_br_data,
df1 = OlinkAnalyze:::data_ht_small,
df2 = OlinkAnalyze:::data_3k_small,
df1_project_nr = "Explore HT",
df2_project_nr = "Explore 3072",
reference_project = "Explore HT")

OlinkAnalyze documentation built on April 4, 2025, 3:26 a.m.