| ansi_collapse_quot | Utility function that adds quotation marks on elements... |
| assign_subject2plate | assign subject to a plate for longitudinal randomization |
| check_checksum | Help function comparing the checksum reported by Olink... |
| check_col_key | Check if col_key is valid. |
| check_columns | Check presence of columns in dataset. |
| check_darid | Help function checking for DARID and PanelDataArchiveVersion... |
| check_file_exists | Help function checking if file exists. |
| check_file_extension | Help function checking if file extension is acceptable. |
| check_ht_fixed_lod_version | Help function to check Explore HT Fixed LOD file version |
| check_is_arrow_object | Help function checking if a variable is an R6 ArrowObject. |
| check_is_boolean | Help function checking if a variable is a vector of booleans. |
| check_is_character | Help function checking if a variable is a vector of... |
| check_is_dataset | Help function checking if a variable is a tibble or an... |
| check_is_integer | Help function checking if a variable is a vector of integers. |
| check_is_list | Help function checking if a variable is a list. |
| check_is_numeric | Help function checking if a variable is a vector of numerics. |
| check_is_scalar_boolean | Help function checking if a variable is a scalar boolean. |
| check_is_scalar_character | Help function checking if a variable is a scalar character. |
| check_is_scalar_integer | Help function checking if a variable is a scalar integer. |
| check_is_scalar_numeric | Help function checking if a variable is a scalar numeric |
| check_is_tibble | Help function checking if a variable is a tibble dataset. |
| check_library_installed | Help function to check if suggested libraries are installed... |
| check_log_colname | Check if check_log has identified required column in the... |
| check_npx | Check NPX data format |
| check_npx_all_na_assays | Help function to identify Olink assays with all quantified... |
| check_npx_all_na_sample | Help function to identify Olink samples with all quantified... |
| check_npx_col_class | Help function checking types of columns in data. |
| check_npx_col_names | Check, update and define column names used in downstream... |
| check_npx_duplicate_sample_ids | Help function checking for duplicate sample identifiers in... |
| check_npx_nonunique_uniprot | Help function checking for assays mapping to multiple UniProt... |
| check_npx_olinkid | Help function checking whether df contains invalid Olink... |
| check_npx_qcwarn_assays | Help function checking data for assay QC warnings. |
| check_npx_update_col_names | Update column names to be used in downstream analyses |
| check_olink_broader_platform | Help function checking that broad_platform is expected. |
| check_olink_data_type | Help function checking that data_type is expected. |
| check_olink_platform | Help function checking that olink_platform is expected. |
| check_olink_quant_type | Help function checking that data_type is expected. |
| check_osi | Utility function to check OSI values for validity |
| check_out_df_arg | Help function checking that the requested output class of the... |
| clean_npx | Clean proteomics data quantified with Olink's PEA technology |
| convert_read_npx_output | Help function converting the output dataset from read_npx*... |
| dot-check_params | Common parameters for check functions. |
| dot-downstream_fun_args | Common parameters for downstream analysis functions. |
| dot-get_olink_data_details | Common parameters for getter functions in this file. |
| dot-read_npx_args | Common parameters for read_npx-related functions. |
| generate_plate_holder | Create empty plate layout |
| get_all_olink_broader_platforms | Get names of all broader Olink platforms. |
| get_all_olink_data_types | Get names of all Olink quantification methods (data types). |
| get_all_olink_platforms | Get names of all Olink platforms. |
| get_all_olink_quant_types | Get names of all Olink quantification types. |
| get_alt_colnames | Gets alternative column names for a given column key. |
| get_checksum_file | Help function to get the file name of the checksum file from... |
| get_df_output_print | Prints class type output from read_npx* functions. |
| get_field_separator | Help function to get the separator of a delimited file... |
| get_file_ext | Gets all file extensions based on the file format. |
| get_file_ext_summary | Describes acceptable file extension for each file type. |
| get_file_formats | Get all acceptable file formats. |
| get_npx_file | Help function to get the file name of the Olink data file... |
| get_olink_broader_platforms | Get names of selected broader Olink platforms. |
| get_olink_data_types | Get names of selected Olink quantification methods (data... |
| get_olink_platforms | Get names of selected Olink platforms. |
| get_olink_quant_types | Get names of selected Olink quantification types. |
| manifest | Example Sample Manifest |
| mapping_file_id | Identifying which mapping file to use |
| norm_internal_adjust | Combine reference and non-reference datasets |
| norm_internal_adjust_not_ref | Add adjustment factors to a dataset |
| norm_internal_adjust_ref | Modify the reference dataset to be combined with the... |
| norm_internal_assay_median | Compute median value of the quantification method for each... |
| norm_internal_bridge | Internal bridge normalization function |
| norm_internal_cross_product | Internal function normalizing Olink Explore 3k to Olink... |
| norm_internal_reference_median | Internal reference median normalization function |
| norm_internal_rename_cols | Update column names of non-reference dataset based on those... |
| norm_internal_subset | Internal subset normalization function |
| norm_internal_update_maxlod | Update MaxLOD to the maximum MaxLOD across normalized... |
| npx_data1 | NPX Data in Long format. |
| npx_data2 | NPX Data in Long format, a 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_bridgeability_plot | Plots for each bridgeable assays between two products. |
| olink_bridge_selector | Bridge selection function |
| olink_color_discrete | Olink color scale for discrete ggplots |
| olink_color_gradient | Olink color scale for continuous ggplots |
| olink_display_plate_dist | Plot distributions of a given variable for all plates |
| olink_display_plate_layout | 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_format_oid_no_overlap | Retrieve non-overlapping assays between two NPX datasets |
| olink_format_rm_ext_ctrl | Remove negative controls and plate controls from dataset. For... |
| olink_heatmap_plot | Function to plot a heatmap of the NPX data |
| olink_iqr | Compute inter-quartile range (IQR) of multiplied by a fixed... |
| olink_lmer | Function that performs a linear mixed model per protein. |
| olink_lmer_plot | Function which performs a point-range plot per protein on a... |
| olink_lmer_posthoc | Function which performs a linear mixed model posthoc per... |
| olink_lod | Calculate LOD using Negative Controls or Fixed LOD |
| olink_median | Compute median of quantified value |
| olink_median_iqr_outlier | Compute outliers based on median +/- iqr_sd * IQR |
| olink_normalization | Normalize two Olink datasets |
| olink_normalization_bridge | Bridge normalization of all proteins between two NPX... |
| olink_normalization_bridgeable | Identify if assays shared between Olink Explore 3072 and... |
| olink_normalization_format | Format the output of olink_normalization for seamless use... |
| olink_normalization_n | Bridge and/or subset normalization of all proteins among... |
| olink_normalization_n_check | An internal function to perform checks on the input of the... |
| olink_normalization_project_name_check | An internal function to perform checks on the input project... |
| olink_normalization_qs | Quantile smoothing normalization of all proteins between two... |
| olink_normalization_sample_check | An internal function to perform checks on the input samples... |
| olink_normalization_subset | Subset normalization of all proteins between two NPX... |
| olink_norm_input_assay_overlap | Check datasets and reference_medians for Olink identifiers... |
| olink_norm_input_check | Check inputs of 'olink_normalization' function. |
| olink_norm_input_check_df_cols | Check columns of a list of datasets to be normalized. |
| olink_norm_input_check_samples | Check reference samples to be used for normalization |
| olink_norm_input_class | Check classes of input in olink_normalization function |
| olink_norm_input_clean_assays | Check datasets and reference_medians for unexpected Olink... |
| olink_norm_input_cross_product | Check if bridge or cross-platform normalization |
| olink_norm_input_norm_method | Check datasets and reference_medians for Olink identifiers... |
| olink_norm_input_ref_medians | Check datasets of reference_medians |
| olink_norm_input_validate | Validate inputs of normalization function |
| olink_norm_product_id | Identify names of product for each project |
| olink_norm_reference_id | Identify reference project. |
| olink_one_non_parametric | Function which performs a Kruskal-Wallis Test or Friedman... |
| olink_one_non_parametric_posthoc | Function which performs posthoc test per protein for the... |
| olink_ordinal_regression | Function that performs a two-way ordinal analysis. |
| olink_ordinal_regression_posthoc | Function which performs an posthoc test per protein. |
| olink_osi_dist_plot | OSI distribution plot |
| olink_pal | Olink color panel for plotting |
| olink_pathway_enrichment | Performs pathway enrichment using over-representation... |
| olink_pathway_heatmap | Creates a heatmap of proteins related to pathways using... |
| olink_pathway_visualization | Creates bargraph of top/selected enrichment terms from GSEA... |
| 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 |
| product_to_platesize | Check product name and set plate size accordingly |
| read_npx | Read Olink data in R. |
| read_npx_delim | Help function to read long or wide format "Ct", "NPX", or... |
| read_npx_delim_long | Help function to read long format "Ct", "NPX", or... |
| read_npx_delim_wide | Help function to read wide format "Ct", "NPX", or... |
| read_npx_excel | Help function to read long or wide format "Ct", "NPX", or... |
| read_npx_format | Help function to read excel and delimited Olink data files in... |
| read_npx_format_colnames | Help function checking whether a dataset contains NA or empty... |
| read_npx_format_get_format | Help function to determine the format (wide or long) of the... |
| read_npx_format_get_platform | Help function to determine the Olink platform from the input... |
| read_npx_format_get_quant | Help function to determine the type of quantification from... |
| read_npx_format_read | Help function to read excel and delimited Olink data files in... |
| read_npx_legacy | Olink legacy function for reading NPX or absolute... |
| read_npx_legacy_check | Help function ensuring 'read_npx_legacy' works |
| read_npx_legacy_help | Help function utilizing functions from 'read_npx_format' and... |
| read_npx_parquet | Help function to read NPX data from long format parquet Olink... |
| read_npx_wide | Convert Olink data in wide format with "Ct", "NPX", and... |
| read_npx_wide_bottom | Convert the bottom matrix from Olink dataset in wide format... |
| read_npx_wide_bottom_version | Additional checks of the bottom matrix of Olink dataset in... |
| read_npx_wide_check_top | Additional checks of the top matrix of Olink dataset in wide... |
| read_npx_wide_middle | Split the middle matrix from Olink dataset in wide format. |
| read_npx_wide_npxs_version | Extract version of NPX Signature from the head matrix of... |
| read_npx_wide_panel_version | Help function to extract Panel_Version from Panel column. |
| read_npx_wide_split_row | Split Olink wide files to sub-matrices. |
| read_npx_wide_top | Split the top matrix from Olink dataset in wide format. |
| read_npx_zip | Help function to read "Ct", "NPX", and "Quantified" data from... |
| red_npx_wide_top_mid_long | Combine top and middle matrices in long format. |
| remove_all_na_cols | Utility function removing columns with all values NA from a... |
| run_check_npx | Check and run 'check_npx()' if not provided. |
| set_plot_theme | Function to set plot theme |
