run_check_npx: Check and run 'check_npx()' if not provided.
In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

run_check_npx

R Documentation

Check and run `check_npx()` if not provided.

Description

Check and run check_npx() if not provided.

Usage

run_check_npx(df, check_log = NULL)

Arguments

`df`	A "tibble" or "ArrowObject" from `read_npx`.
`check_log`	A named list returned by `check_npx()`. If `NULL`, `check_npx()` will be run internally using `df`.

Details

This function acts as a wrapper for check_npx(). It will check if the input check_log provided by the user is valid. If not, it will throw relevant errors or warnings. Alternatively, if check_log was not provided by the user, it will run check_npx() to provide check_log to enable downstream functions to run.#'

Value

A list containing the following elements:

col_names List of column names from the input data frame marking the columns to be used in downstream analyses.
oid_invalid Character vector of invalid OlinkID.
assay_na Character vector of assays with all samples having NA values.
sample_id_dups Character vector of duplicate SampleID.
sample_id_na Character vector containing SampleID of samples with quantified values NA for all assays.
col_class Data frame with columns of incorrect type including column key col_key, column name col_name, detected column type col_class and expected column type expected_col_class.
assay_qc Character vector containing OlinkID of assays with at least one assay warning.
non_unique_uniprot Character vector of OlinkID mapped to more than one UniProt ID.
darid_invalid Character vector containing outdated combinations of DataAnalysisRefID and PanelDataArchiveVersion.