olink_norm_input_check: Check inputs of 'olink_normalization' function.

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Check inputs of olink_normalization function.

Description

This function is a wrapper of multiple help functions which check the inputs of the olink_normalization function.

Usage

olink_norm_input_check(
  df1,
  df2,
  overlapping_samples_df1,
  overlapping_samples_df2,
  df1_project_nr,
  df2_project_nr,
  reference_project,
  reference_medians
)

Arguments

df1	First dataset to be used in normalization (required).
df2	Second dataset to be used in normalization.
overlapping_samples_df1	Samples to be used for adjustment factor calculation in df1 (required).
overlapping_samples_df2	Samples to be used for adjustment factor calculation in df2.
df1_project_nr	Project name of first dataset (df1).
df2_project_nr	Project name of first dataset (df2).
reference_project	Project name of reference_project. Should be one of df1_project_nr or df2_project_nr. Indicates the project to which the other project is adjusted to.
reference_medians	Dataset with columns "OlinkID" and "Reference_NPX". Used for reference median normalization.

Details

The following checks are performed:

• olink_norm_input_validate:

  • Determines the normalization to be performed by intersecting inputs with internal global variable olink_norm_mode_combos.

  • Returns the type of normalization to be performed from olink_norm_modes.

  • Message with the normalization type.

  • Error message if input is invalid.

• olink_norm_input_class:

  • Checks if all inputs are of the expected class:

    • df1, df2 and reference_medians: tibble or R6 ArrowObject

    • overlapping_samples_df1, overlapping_samples_df2, df1_project_nr, df2_project_nr and reference_project: Character vector

  • Also checks the validity of names of project and reference project.

  • Error if invalid input classes are detected.

• olink_norm_input_check_df_cols:

  • Detects the column names of input datasets df1 and df2 to allow for alternative names.

  • Returns named list of column names to use downstream.

  • Warning if Normalization column missing from all datasets.

  • Warning if LOD is missing or if there are multiple LOD columns.

  • Error if required columns are missing.

  • Error if not all input datasets have or lack Normalization column.

  • Error if input datasets have been quantified with different methods.

• olink_norm_input_ref_medians:

  • Checks validity of dataset containing reference_medians.

  • Error if required columns are missing based on olink_norm_ref_median_cols.

  • Error if columns are not of the correct class bases on olink_norm_ref_median_cols.

  • Error if there duplicate assay identifiers.

• olink_norm_input_check_samples:

  • Check character vectors of reference sample identifiers for:

    • Being present in df1 and/or df2.

    • Duplicate identifiers.

• olink_norm_input_clean_assays:

  • Returns a named list with the updated df1, df2 and/or reference_medians.

  • Removes assays that are not of the format OID followed by 5 digits.

  • Removes assays that are marked with Normalization = EXCLUDED.

• olink_norm_input_assay_overlap:

  • Returns a named list with the updated df1, df2 and/or reference_medians.

  • Remove assays not shared between df1 and df2, or between df1 and reference_medians.

• olink_norm_input_norm_method:

  • Check if all assays in df1 and df2 have been originally normalized with the same method "Intensity" or "Plate control".

  • Warning is thrown if not.

Value

Named list of updated inputs to use for normalization:

• df1: dataset df1.

• df2: NULL if reference median normalization, or dataset df2.

• overlapping_samples_df1: character vector of reference samples from df1.

• overlapping_samples_df2: NULL if reference median normalization, or character vector of reference samples from df1.

• df1_project_nr: name of df1 project.

• df2_project_nr: NULL if reference median normalization, or name of df2 project.

• reference_project: NULL if reference median normalization, or name of reference project.

• reference_medians: NULL if bridge or subset normalization, or dataset with reference_medians.

• df1_cols: column names of df1 to use downstream.

• df2_cols: NULL if reference median normalization, or column names of df2 to use downstream.

• norm_mode: one of bridge, subset, ref_median, and norm_cross_product indicating the normalization to be performed.

Author(s)

Klev Diamanti

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