calculate_pw_scores

a data frame that must contain the 3 columns below:<dl class="dl-horizontal">
 <dt>Pathway</dt><dd>Description of the enriched pathway</dd>
 <dt>Up_regulated</dt><dd>the up-regulated genes in the input involved in the given pathway, comma-separated</dd>
 <dt>Down_regulated</dt><dd>the down-regulated genes in the input involved in the given pathway, comma-separated</dd>
</dl>

pw_table

the gene expression/methylation matrix. Columns are samples
and rows are genes. Column names must contain sample names and row names must
contain the gene symbols.

exp_mat

(Optional) A vector of sample names that are cases in the
case/control experiment.

cases

Boolean value to indicate whether or not to draw the
heatmap plot of the scores. (default = TRUE)

plot_hmap

Additional arguments for `plot_scores` for aesthetics of the heatmap plot

Calculate Pathway Scores for Each Subject

Pathway enrichment analysis enables researchers to uncover mechanisms
underlying the phenotype. pathfindR is a tool for pathway enrichment analysis
utilizing active subnetworks. It identifies active subnetworks in a
protein-protein interaction network using user-provided a list of genes.
It performs pathway enrichment analyses on the identified subnetworks.
pathfindR also offers functionalities to cluster enriched pathways and identify
representative pathways and to score the pathways per sample. The method is
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R
Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv.
<doi:10.1101/272450>.

Ege Ulgen

pathfindR

Pathway Enrichment Analysis Utilizing Active Subnetworks

calculate_pw_scores function

a data frame that must contain the 3 columns below:<dl class='dl-horizontal'>
 <dt>Pathway</dt><dd>Description of the enriched pathway</dd>
 <dt>Up_regulated</dt><dd>the up-regulated genes in the input involved in the given pathway, comma-separated</dd>
 <dt>Down_regulated</dt><dd>the down-regulated genes in the input involved in the given pathway, comma-separated</dd>
</dl>

calculate_pw_scores: Calculate Pathway Scores for Each Subject

Description

Usage

Arguments

Value

Examples