OlinkAnalyze4.3.1 package

Check data completeness

Identifying which mapping file to use

Add adjustment factors to a dataset

Modify the reference dataset to be combined with the non-reference nor...

Combine reference and non-reference datasets

Compute median value of the quantification method for each Olink assay

Internal bridge normalization function

Internal function normalizing Olink Explore 3k to Olink Explore 3072

Internal reference median normalization function

Update column names of non-reference dataset based on those of referen...

Internal subset normalization function

Update MaxLOD to the maximum MaxLOD across normalized datasets.

Function which performs an ANOVA posthoc test per protein.

Function which performs an ANOVA per protein

Function which plots boxplots of selected variables

Plots for each bridgeable assays between two products.

Bridge selection function

Olink color scale for discrete ggplots

Olink color scale for continuous ggplots

Plot distributions of a given variable for all plates

Plot all plates colored by a variable

Function to plot the NPX distribution by panel

Olink fill scale for discrete ggplots

Olink fill scale for continuous ggplots

Function to plot a heatmap of the NPX data

Compute inter-quartile range (IQR) of multiplied by a fixed value

Function which performs a point-range plot per protein on a linear mix...

Function which performs a linear mixed model posthoc per protein.

Function which performs a linear mixed model per protein

Calculate LOD using Negative Controls or Fixed LOD

Compute outliers based on median +/- iqr_sd * IQR

Compute median of quantified value

Check datasets and reference_medians for Olink identifiers not shared ...

Check columns of a list of datasets to be normalized.

Check reference samples to be used for normalization

Check inputs of olink_normalization function.

Check classes of input in olink_normalization function

Check datasets and reference_medians for unexpected Olink identifiers ...

Check if bridge or cross-platform normalization

Check datasets and reference_medians for Olink identifiers not shared ...

Check datasets of reference_medians

Validate inputs of normalization function

Identify names of product for each project

Identify reference project.

Bridge normalization of all proteins between two NPX projects.

Identify if assays shared between Olink Explore 3072 and Olink Explore...

An internal function to perform checks on the input of the function ol...

Bridge and/or subset normalization of all proteins among multiple NPX ...

Formatting the output of olink_normalization_product for seamless use ...

An internal function to perform checks on the input project names in t...

Quantile smoothing normalization of all proteins between two NPX proje...

An internal function to perform checks on the input samples in the fun...

Subset normalization of all proteins between two NPX projects.

Normalize two Olink datasets

Function which performs posthoc test per protein for the results from ...

Function which performs a Kruskal-Wallis Test or Friedman Test per pro...

Function which performs an posthoc test per protein.

Function which A two-way ordinal analysis of variance can address an e...

Olink color panel for plotting

Performs pathway enrichment using over-representation analysis (ORA) o...

Creates a heatmap of selected pathways and proteins

Creates bargraph of top/selected enrichment terms from GSEA or ORA res...

Function to plot a PCA of the data

Randomly assign samples to plates

Function to plot an overview of a sample cohort per Panel

Function which performs a t-test per protein

Function to make a UMAP plot from the data

Easy volcano plot with Olink theme

Function which performs a Mann-Whitney U Test per protein

Pipe operator

Capture the output of printing an object

Read in flex data

Helper function to read in Olink Explore csv or txt files

Helper function to read in Olink Explore parquet output files

Helper function to read in Olink Explore zip csv files

Function to read NPX data into long format

Function to set plot theme