check_data_completeness |
Check data completeness |
manifest |
Example Sample Manifest |
npx_data1 |
NPX Data in Long format |
npx_data2 |
NPX Data in Long format, Follow-up |
olink_anova |
Function which performs an ANOVA per protein |
olink_anova_posthoc |
Function which performs an ANOVA posthoc test per protein. |
olink_boxplot |
Function which plots boxplots of selected variables |
olink_bridgeselector |
Bridge selection function |
olink_color_discrete |
Olink color scale for discrete ggplots |
olink_color_gradient |
Olink color scale for continuous ggplots |
olink_displayPlateDistributions |
Plot distributions of a given variable for all plates |
olink_displayPlateLayout |
Plot all plates colored by a variable |
olink_dist_plot |
Function to plot the NPX distribution by panel |
olink_fill_discrete |
Olink fill scale for discrete ggplots |
olink_fill_gradient |
Olink fill scale for continuous ggplots |
olink_heatmap_plot |
Function to plot a heatmap of the NPX data |
olink_lmer |
Function which performs a linear mixed model per protein |
olink_lmer_plot |
Function which performs a point-range plot per protein on a linear mixed model |
olink_lmer_posthoc |
Function which performs a linear mixed model posthoc per protein. |
olink_lod |
Calculate LOD using Negative Controls or Fixed LOD |
olink_normalization |
Normalization of all proteins (by OlinkID). |
olink_normalization_bridge |
Bridge normalization of all proteins between two NPX projects. |
olink_normalization_n |
Bridge and/or subset normalization of all proteins among multiple NPX projects. |
olink_normalization_n_check |
An internal function to perform checks on the input of the function olink_normalization_n. |
olink_normalization_project_name_check |
An internal function to perform checks on the input project names in the functions olink_normalization_bridge and olink_normalization_subset. The function is expected to run all checks on project names to make sure that normalization can be performed smoothly. It should work independently of the function calling it. |
olink_normalization_sample_check |
An internal function to perform checks on the input samples in the functions olink_normalization_bridge and olink_normalization_subset. The function is expected to run all checks on SampleID to make sure that normalization can be performed smoothly. It should work independently of the function calling it. |
olink_normalization_subset |
Subset normalization of all proteins between two NPX projects. |
olink_one_non_parametric |
Function which performs a Kruskal-Wallis Test or Friedman Test per protein |
olink_one_non_parametric_posthoc |
Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test. |
olink_ordinalRegression |
Function which A two-way ordinal analysis of variance can address an experimental design with two independent variables, each of which is a factor variable. The main effect of each independent variable can be tested, as well as the effect of the interaction of the two factors. |
olink_ordinalRegression_posthoc |
Function which performs an posthoc test per protein. |
olink_pal |
Olink color panel for plotting |
olink_pathway_enrichment |
Performs pathway enrichment using over-representation analysis (ORA) or gene set enrichment analysis (GSEA) |
olink_pathway_heatmap |
Creates a heatmap of selected pathways and proteins |
olink_pathway_visualization |
Creates bargraph of top/selected enrichment terms from GSEA or ORA results from olink_pathway_enrichment() |
olink_pca_plot |
Function to plot a PCA of the data |
olink_plate_randomizer |
Randomly assign samples to plates |
olink_qc_plot |
Function to plot an overview of a sample cohort per Panel |
olink_ttest |
Function which performs a t-test per protein |
olink_umap_plot |
Function to make a UMAP plot from the data |
olink_volcano_plot |
Easy volcano plot with Olink theme |
olink_wilcox |
Function which performs a Mann-Whitney U Test per protein |
print_and_capture |
Capture the output of printing an object |
read_flex |
Read in flex data |
read_NPX |
Function to read NPX data into long format |
read_npx_csv |
Helper function to read in Olink Explore csv or txt files |
read_npx_parquet |
Helper function to read in Olink Explore parquet output files |
read_npx_zip |
Helper function to read in Olink Explore zip csv files |
set_plot_theme |
Function to set plot theme |