Report Modules: panoply_cna_correlation_report

panoply_cna_correlation_report

Description

This module creates an R Markdown report for the panoply_cna_correlation module.

The report provides:

• A genome-wide heatmap depicting significant (FDR < fdr) cis and trans correlation between CNA-RNA and CNA-type.

• A table providing a high level summary about the total number of genes that were used the analysis, number of significant genes (FDR < fdr), number of significant events (cis + trans) and the number of significant cis effects.

Input

Required inputs:

• tarball: (.tar file) tarball from panoply_cna_correlation
• config_yaml: (.yaml file) master-parameters.yaml
• label: (String) label used in the report title
• type: (String) data (-ome) type
• tmpDir: (String, default="tmp") name of directory used to extract the tarball

yaml-exclusive parameters:

panoply_cna_correlation_report

• fdr: (Float, default = 0.05) FDR value used to define signifcance.

Output

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