pichairaman/ompare

Omics Patient Report

Omics Patient Report

Authors:	Pichai Raman Komal S Rathi
Contact:	[email protected]
Organization:	D3B, CHOP
Status:	This is "work in progress"
Date:	2024-09-16

Prerequisites

# install packages
Rscript code/install_pkgs.R

Input files

Instructions:

• Create project folder under data/.
• Keep the subdirectory names and file extensions consistent.
• Run script to create and organize project folder:

Rscript create_project.R <path to project directory with all files>

# This should create a folder structure as shown below:

# Directory structure:
data/PNOC008
├── CNV
│   └── 8a03c927-7f37-4605-ba6e-73a885cade6c.CNVs
├── Clinical
│   └── patient_report.txt
├── ExpressionGene
│   └── 7316-903_577716.genes.results
├── Fusions
│   ├── 7316-535.local.transcript.converted.pe.star-fusion.fusion_candidates.final
│   └── eb06d52a-110b-4c0e-9e90-94ea68d2f698.arriba.fusions.tsv
├── ImmuneScores
│   └── rawScores.txt
├── MutationsMAF
│   ├── 5c3eace5-950a-4a05-81ed-5c04b4a0a367.strelka.vep.maf
│   ├── 8a03c927-7f37-4605-ba6e-73a885cade6c.strelka.vep.maf
│   └── ae4ce725-d3c4-455d-822e-6c5067444b5e.strelka.vep.maf
└── tmpRCircos.png

• Files provided by user:

  • CNV/*.CNVs (Optional)
  • Clinical/patient_report.txt (Optional)
  • ExpressionGene/*.genes.results (Optional)
  • Fusions/*.arriba.fusions.tsv (Optional)
  • Fusions/*.star-fusion.fusion_candidates.final (Optional)
  • MutationsMAF/*.maf (Optional)

• Files created upon execution:

  • tmpRCircos.png. Requires Fusion data.
  • ImmuneScores/rawScores.txt. Requires Expression data.

Running the code

Input Parameters:

• topDir is your project directory. (Required)
• fusion_method is the fusion method. Allowed values: star, arriba, both or not specified. (Optional)
• set_title is the title for the report. (Optional)

# run with custom parameter values
rmarkdown::render(input = 'OMPARE.Rmd',
                  params = list(topDir = 'data/PNOC008/',
                  fusion_method = 'arriba',
                  set_title = 'PNOC008 Report'))