olink_bridgeselector: Bridge selection function

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Bridge selection function

Description

The bridge selection function will select a number of bridge samples based on the input data. It selects samples with good detection, which passes QC and cover a good range of the data. If possible, Olink recommends 8-16 bridge samples. When running the selector, Olink recommends starting at sampleMissingFreq = 0.10 which represents a maximum of 10% data below LOD per sample. If there are not enough samples output, increase to 20%.

The function accepts NPX Excel files with data < LOD replaced.

Usage

olink_bridgeselector(df, sampleMissingFreq, n)

Arguments

df	Tibble/data frame in long format such as produced by the Olink Analyze read_NPX function.
sampleMissingFreq	The threshold for sample wise missingness.
n	Number of bridge samples to be selected.

Value

A "tibble" with sample IDs and mean NPX for a defined number of bridging samples. Columns include:

• SampleID: Sample ID

• PercAssaysBelowLOD: Percent of Assays that are below LOD for the sample

• MeanNPX: Mean NPX for the sample

Examples

bridge_samples <- olink_bridgeselector(npx_data1, sampleMissingFreq = 0.1, n = 20)

OlinkAnalyze documentation built on Nov. 4, 2023, 1:07 a.m.