synthetic_metadata

A dataset containing sample clinical data for 100 patients with 40%
response rate

datasets

Performs multi-omic differential network
analysis by revealing differential interactions between molecular entities
(genes, proteins, transcription factors, or other biomolecules) across the
omic datasets provided.
For each omic dataset, a differential network is constructed where
links represent statistically significant differential interactions between
entities. These networks are then integrated into a comprehensive visualization
using distinct colors to distinguish interactions from different omic layers.
This unified display allows interactive exploration of cross-omic
patterns, such as differential interactions present at both transcript and
protein levels. For each link, users can access differential statistical
significance metrics (p values or adjusted p values, calculated via robust or
traditional linear regression with interaction term) and differential regression
plots.
The methods implemented in this package are described in Sciacca et al. (2023)
<doi:10.1093/bioinformatics/btad192>.

Elisabetta Sciacca

multiDEGGs

Multi-Omic Differentially Expressed Gene-Gene Pairs

Myles Lewis

synthetic_metadata function

A data frame with 100 rows and 4 columns (IDs are in rownames):<dl>
<dt>patient_id</dt>
<dd>IDs matching the IDs used in the colnames of the assay
data matrix/matrices.</dd><dt>age</dt>
<dd>A column to simulate age of patients. Not used.</dd><dt>gender</dt>
<dd>A column to simulate gender of patients. Not used.</dd><dt>response</dt>
<dd>The response outcome, to be used for differential analysis</dd>
</dl>

Format

Synthetic clinical data — synthetic_metadata

A data frame with 100 rows and 4 columns (IDs are in rownames):<dl>
<dt>patient_id</dt>
<dd>IDs matching the IDs used in the colnames of the assay
data matrix/matrices.</dd>

<dt>age</dt>
<dd>A column to simulate age of patients. Not used.</dd>

<dt>gender</dt>
<dd>A column to simulate gender of patients. Not used.</dd>

<dt>response</dt>
<dd>The response outcome, to be used for differential analysis</dd>


</dl>

synthetic_metadata: Synthetic clinical data

Description

Arguments

Format