olink_norm_input_clean_assays

Check <var>datasets</var> and <var>reference_medians</var> for unexpected Olink
identifiers or excluded assays

A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.

Kathleen Nevola

OlinkAnalyze

Facilitate Analysis of Proteomic Data from Olink

Marianne Sandin

Jamey Guess

Simon Forsberg

Christoffer Cambronero

Pascal Pucholt

Boxi Zhang

Masoumeh Sheikhi

Klev Diamanti

Amrita Kar

Lei Conze

Kristyn Chin

Danai Topouza

Stephen Pollo

Kang Dong

Kristian Hodén

Per Eriksson

Nicola Moloney

Britta Lötstedt

Emmett Sprecher

Jessica Barbagallo

Olof Mansson

Ola Caster

Olink 

olink_norm_input_clean_assays function

<dl><dt>lst_df</dt>
<dd>Named list of datasets to be normalized.</dd>
<dt>reference_medians</dt>
<dd>Dataset with columns "OlinkID" and "Reference_NPX".
Used for reference median normalization.</dd>
<dt>lst_cols</dt>
<dd>Named list of vectors with the required column names for each
dataset in <var>lst_df</var>.</dd>
<dt>norm_mode</dt>
<dd>Character string indicating the type of normalization to be
performed. Expecting one of
bridge, subset, ref_median or norm_cross_product. # nolint</dd></dl>

Arguments

Author

Check datasets and reference_medians for unexpected Olink
identifiers or excluded assays — olink_norm_input_clean_assays

<dl>

<dt>lst_df</dt>
<dd>Named list of datasets to be normalized.</dd>


<dt>reference_medians</dt>
<dd>Dataset with columns "OlinkID" and "Reference_NPX".
Used for reference median normalization.</dd>


<dt>lst_cols</dt>
<dd>Named list of vectors with the required column names for each
dataset in <var>lst_df</var>.</dd>


<dt>norm_mode</dt>
<dd>Character string indicating the type of normalization to be
performed. Expecting one of
bridge, subset, ref_median or norm_cross_product. # nolint</dd>

</dl>

Check <var>datasets</var> and <var>reference_medians</var> for unexpected Olink
identifiers or excluded assays

olink_norm_input_clean_assays: Check `datasets` and `reference_medians` for unexpected Olink identifiers or excluded assays

Description

Usage

Value

Arguments

Author