From 8e7432cef83da26dc539e43b390f726a22be0238 Mon Sep 17 00:00:00 2001
From: jharenza <jharenza@gmail.com>
Date: Mon, 3 Jun 2024 18:43:15 +0000
Subject: [PATCH] add readme and shell script

---
 analyses/braf-fusions/README.md       | 71 +++++++++++++++++++++++++++
 analyses/braf-fusions/run-analysis.sh | 10 ++++
 2 files changed, 81 insertions(+)
 create mode 100644 analyses/braf-fusions/README.md
 create mode 100644 analyses/braf-fusions/run-analysis.sh

diff --git a/analyses/braf-fusions/README.md b/analyses/braf-fusions/README.md
new file mode 100644
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+++ b/analyses/braf-fusions/README.md
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+# BRAF fusions and survival by cluster
+
+Module authors: Ryan Corbett (@rjcorb), Jo Lynne Rokita (@jharenza)
+
+The purpose of this module is to assess survival in imaging clusters +/- BRAF fusion type
+
+## Usage
+### script to run analysis
+<br>**Run shell script to make final tables to be used for plotting below**
+```
+bash run-analysis.sh
+```
+Input files:
+```
+../../data/fusion-dgd.tsv.gz
+../../data/histologies.tsv
+20231003_merged_imaging_clustering_risk_stratification.xlsx
+imaging_clustering_cohort.csv
+```
+
+## Folder content
+* `run-analysis.sh` shell script to run analysis
+* `01-fusion-breakpoints-by-imaging-cluster.Rmd` Assess prevalence of BRAF fusion by cluster 
+* `02-imaging-cluster-survival.Rmd` Assess survival based on imaging cluster and/or BRAF fusion type
+
+## Directory structure
+```
+.
+├── 01-fusion-breakpoints-by-imaging-cluster.Rmd
+├── 01-fusion-breakpoints-by-imaging-cluster.html
+├── 02-imaging-cluster-survival.Rmd
+├── 02-imaging-cluster-survival.html
+├── README.md
+├── input
+│   ├── 20231003_merged_imaging_clustering_risk_stratification.xlsx
+│   └── imaging_clustering_cohort.csv
+├── plots
+│   ├── breakpoint-group-by-cluster-ht.pdf
+│   ├── breakpoint-type-by-cluster-ht.pdf
+│   ├── imaging_forest_efs_braf_add_resection_cluster.pdf
+│   ├── imaging_forest_efs_braf_add_resection_cluster_group.pdf
+│   ├── imaging_forest_efs_braf_add_resection_cluster_type.pdf
+│   ├── imaging_forest_efs_int_resection_fusion_cluster.pdf
+│   ├── imaging_forest_efs_int_resection_subtype_cluster.pdf
+│   ├── imaging_forest_efs_nonbraf_add_resection_cluster.pdf
+│   ├── km_efs_imaging_braf_breakpoint_group.pdf
+│   ├── km_efs_imaging_braf_breakpoint_type.pdf
+│   ├── km_efs_imaging_braf_cluster.pdf
+│   ├── km_efs_imaging_braf_molecular_subtype.pdf
+│   ├── km_efs_imaging_cluster.pdf
+│   └── km_efs_imaging_nonbraf_cluster.pdf
+├── results
+│   ├── braf-fusion-breakpoints-by-patient.tsv
+│   ├── coxph_imaging_braf_efs_add_resection_cluster.RDS
+│   ├── coxph_imaging_efs_int_resection_fusion_cluster.RDS
+│   ├── coxph_imaging_efs_int_resection_subtype_cluster.RDS
+│   ├── coxph_imaging_nonbraf_efs_add_resection_cluster.RDS
+│   ├── coxph_imaging_nonbraf_efs_add_resection_cluster_breakpoint_group.RDS
+│   ├── coxph_imaging_nonbraf_efs_add_resection_cluster_breakpoint_type.RDS
+│   ├── imaging_clusters_plus_subtypes_breakpoints.tsv
+│   ├── imaging_forest_efs_braf_add_resection_cluster.pdf
+│   ├── imaging_forest_efs_braf_add_resection_cluster_type.pdf
+│   ├── imaging_forest_efs_int_resection_fusion_cluster.pdf
+│   ├── imaging_forest_efs_nonbraf_add_resection_cluster.pdf
+│   ├── lgg-braf-fusion-common-breakpoint-freq-image-clusters.tsv
+│   └── lgg-braf-fusion-common-breakpoint-type-image-clusters.tsv
+├── run-analysis.sh
+└── util
+    ├── heatmap_function.R
+    └── survival_models_interaction.R
+```
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diff --git a/analyses/braf-fusions/run-analysis.sh b/analyses/braf-fusions/run-analysis.sh
new file mode 100644
index 0000000..ed295e5
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+++ b/analyses/braf-fusions/run-analysis.sh
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+#!/bin/bash
+
+set -e
+set -o pipefail
+
+# run breakpoint by imaging cluster
+Rscript -e "rmarkdown::render('01-fusion-breakpoints-by-imaging-cluster.Rmd')"
+
+# run survival by imaging cluster
+Rscript -e "rmarkdown::render('02-imaging-cluster-survival.Rmd')"
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