olink_norm_input_class

Check if <var>df1</var>, <var>df2</var> and/or <var>reference_medians</var> are tibble or
ArrowDataset datasets; if <var>overlapping_samples_df1</var> and/or
<var>overlapping_samples_df2</var> are character vectors; and if
<var>df1_project_nr</var>, <var>df2_project_nr</var> and/or <var>reference_project</var> are
scalar character vectors.

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_class function

<dl><dt>df1</dt>
<dd>First dataset to be used in normalization (required).</dd>
<dt>df2</dt>
<dd>Second dataset to be used in normalization.</dd>
<dt>overlapping_samples_df1</dt>
<dd>Samples to be used for adjustment factor
calculation in df1 (required).</dd>
<dt>overlapping_samples_df2</dt>
<dd>Samples to be used for adjustment factor
calculation in df2.</dd>
<dt>df1_project_nr</dt>
<dd>Project name of first dataset (df1).</dd>
<dt>df2_project_nr</dt>
<dd>Project name of first dataset (df2).</dd>
<dt>reference_project</dt>
<dd>Project name of reference_project. Should be one of
<var>df1_project_nr</var> or <var>df2_project_nr</var>. Indicates the project to which
the other project is adjusted to.</dd>
<dt>reference_medians</dt>
<dd>Dataset with columns "OlinkID" and "Reference_NPX".
Used for reference median normalization.</dd>
<dt>norm_mode</dt>
<dd>Scalar character from <var>olink_norm_modes</var> with the
normalization to be performed. Output from
<code>olink_norm_input_validate</code>.</dd></dl>

Arguments

Author

Check classes of input in olink_normalization function — olink_norm_input_class

<dl>

<dt>df1</dt>
<dd>First dataset to be used in normalization (required).</dd>


<dt>df2</dt>
<dd>Second dataset to be used in normalization.</dd>


<dt>overlapping_samples_df1</dt>
<dd>Samples to be used for adjustment factor
calculation in df1 (required).</dd>


<dt>overlapping_samples_df2</dt>
<dd>Samples to be used for adjustment factor
calculation in df2.</dd>


<dt>df1_project_nr</dt>
<dd>Project name of first dataset (df1).</dd>


<dt>df2_project_nr</dt>
<dd>Project name of first dataset (df2).</dd>


<dt>reference_project</dt>
<dd>Project name of reference_project. Should be one of
<var>df1_project_nr</var> or <var>df2_project_nr</var>. Indicates the project to which
the other project is adjusted to.</dd>


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


<dt>norm_mode</dt>
<dd>Scalar character from <var>olink_norm_modes</var> with the
normalization to be performed. Output from
<code>olink_norm_input_validate</code>.</dd>

</dl>

Check classes of input in olink_normalization function

olink_norm_input_class: Check classes of input in olink_normalization function

Description

Usage

Value

Arguments

Author