Report Modules: panoply_ssgsea_report

panoply_ssgsea_report

Description

This module creates an R Markdown report to provide a high-level summary of the panoply_ssgsea module results.

The report provides:

• A heatmap depicting the normalized enrichment scores (NES) of gene sets significant in at least one data column. Significance is defined by parameter fdr in section panoply_ssgsea_report of the cfg_yaml file.

• List of parameters used in the panoply_ssgsea module.

Input

Required inputs:

• tarball: (.tar file) tarball from panoply_ssgsea
• cfg_yaml: (.yaml file) master-parameters.yaml
• label: (String) label used in report title

Optional inputs:

• Heatmap Parameters:
  • fdr: (Float, default=0.05) FDR threshold for heatmap significance stars.
  • top_n: (Int, default=20) max number of significant hits to be plotted on heatmap
  • cluster_rows: (Boolean, default=TRUE) If TRUE, rows will be clustered using distance matrix, with ser_meth as seriation method
  • ser_meth: (String, default='ARSA') Seriation method used for clustering heatmap rows.
  • split_by_prefix: (Boolean) If TRUE, separate heatmaps will be created for pathways with unique prefixes '-<pathway_name>'. Automatically turned on by default for PTM-SEA pathways, but can be manually overridden with this parameter.
  • geneset_groups_file: (.csv file) Optional file used to group related pathways. File must have two columns, with genesets in the first column and geneset-groupings in the second. Geneset names must match the .gmt (gene_set_database) used in panoply_ssgsea.

Output

• report: (.html file) R Markown report.