From fda31f65b1d693bd98ba06e591041997e7405626 Mon Sep 17 00:00:00 2001
From: Dan Miller <dmiller5191@gmail.com>
Date: Tue, 7 Jan 2020 19:58:57 +0000
Subject: [PATCH 1/5] added new fusion summary module updated anaylsis readme
 and ci config

---
 .circleci/config.yml                          |   4 +
 analyses/README.md                            |   1 +
 analyses/fusion-summary/01-fusion-summary.R   | 154 ++++++++++++++++++
 analyses/fusion-summary/README.md             |  19 +++
 .../results/embryomal_fusion_summary.tsv      |   2 +
 .../results/ependymoma_fusion_summary.tsv     |  31 ++++
 analyses/fusion-summary/run-new-analysis.sh   |  22 +++
 7 files changed, 233 insertions(+)
 create mode 100644 analyses/fusion-summary/01-fusion-summary.R
 create mode 100644 analyses/fusion-summary/README.md
 create mode 100644 analyses/fusion-summary/results/embryomal_fusion_summary.tsv
 create mode 100644 analyses/fusion-summary/results/ependymoma_fusion_summary.tsv
 create mode 100644 analyses/fusion-summary/run-new-analysis.sh

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3d74a030ad..0681467c7e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -137,6 +137,10 @@ jobs:
        # - run:
           # name: SNV Caller VAF Cutoff Experiment
           # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/vaf_cutoff_experiment.Rmd', clean = TRUE)"
+
+      - run:
+          name: Fusion Summary
+          command: ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh"
       
  
                 
diff --git a/analyses/README.md b/analyses/README.md
index ed420cb41e..70856dbac8 100644
--- a/analyses/README.md
+++ b/analyses/README.md
@@ -19,6 +19,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
 | [`create-subset-files`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/create-subset-files) | All files | This module contains the code to create the subset files used in continuous integration | All subset files for continuous integration
 | [`focal-cn-file-preparation`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/focal-cn-file-preparation) | `pbta-cnv-cnvkit.seg.gz`, `pbta-cnv-controlfreec.tsv.gz`, `pbta-gene-expression-rsem-fpkm.polya.rds`, `pbta-gene-expression-rsem-fpkm.stranded.rds` | Maps from copy number variant caller segments to gene identifiers; will eventually be updated to use consensus copy number calls ([#186](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/186))| `cnvkit_annotated_cn_autosomes.tsv.gz`, `cnvkit_annotated_cn_x_and_y.tsv.gz`, `controlfreec_annotated_cn_autosomes.tsv.gz`, `controlfreec_annotated_cn_x_and_y.tsv.gz`
 | [`fusion_filtering`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion_filtering) | `pbta-fusion-arriba.tsv.gz`, `pbta-fusion-starfusion.tsv.gz` | Standardizes, filters, and prioritizes fusion calls | `pbta-fusion-putative-oncogenic.tsv`, `pbta-fusion-recurrent-fusion-byhistology.tsv`, `pbta-fusion-recurrent-fusion-bysample.tsv` (included in data download) 
+| [`fusion-summary`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion-summary)| `pbta-histologies.tsv`,`pbta-fusion-putative-oncogenic.tsv` | Generate summary tables from fusion files ([#398](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398)) | N/A
 | [`gene-set-enrichment-analysis`](https://github.com/sjspielman/OpenPBTA-analysis/tree/gene_set_analysis/analyses/gene-set-enrichment-analysis) | `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` and `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds`  | *In progress*. Updated gene set enrichment analysis with appropriate RNA-seq expression data | `results/gsva_scores_stranded.tsv` and `results/gsva_scores_polya.tsv` for stranded, polya expression data respectively  
 | [`independent-samples`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/independent-samples) | `pbta-histologies.tsv` | Generates independent specimen lists for WGS/WXS samples | `independent-specimens.wgs.primary.tsv`, `independent-specimens.wgs.primary-plus.tsv`, `independent-specimens.wgswxs.primary.tsv`, `independent-specimens.wgswxs.primary-plus.tsv` (included in data download)
 | [`interaction-plots`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/interaction-plots) | `independent-specimens.wgs.primary-plus.tsv`, `pbta-snv-consensus-mutation.maf.tsv.gz` | Creates interaction plots for mutation mutual exclusivity/co-occurrence [#13](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/13); may be updated to include other data types (e.g., fusions) | N/A
diff --git a/analyses/fusion-summary/01-fusion-summary.R b/analyses/fusion-summary/01-fusion-summary.R
new file mode 100644
index 0000000000..05f40e9453
--- /dev/null
+++ b/analyses/fusion-summary/01-fusion-summary.R
@@ -0,0 +1,154 @@
+#' @description  Generate fusion files specifically for consumption by molecular subtyping analyses
+#' @author Daniel Miller <millerd15@@email.chop.edu> (D3b)
+#' @note Date: January 2020
+
+suppressPackageStartupMessages(library("dplyr"))
+suppressPackageStartupMessages(library("data.table"))
+suppressPackageStartupMessages(library("optparse"))
+
+#' **Filters**
+#' 
+#' *Demographic Filers*
+#' 1: Used to filter short_histology to get Ependymoma tumors 
+ependSH = "Ependymoma"
+#' 2: Used for Embryonal tumors (short_histology)
+#'  not from ATRT or MB (broad_histology)
+embryBH = "Embryonal tumor"
+embrySH = c("ATRT", "Medulloblastoma")
+#' 
+#' *Fusions Filters*
+#' 1: Exact match a list of fusions common in Ependymoma tumors
+ependFuses = c(
+  "C11orf95--MAML2",
+  "C11orf95--RELA",
+  "C11orf95--YAP1", 
+  "LTBP3--RELA",
+  "PTEN--TAS2R1",
+  "YAP1--FAM118B",
+  "YAP1--MAMLD1",
+  "YAP1--MAMLD2"
+)
+#' 2: Exact match a list of fusions common in Embryonal tumors
+#' as well as fusions containing a particular gene with any other gene
+embryFuses = c(
+  "CIC--NUTM1",
+  "MN1--BEND2",
+  "MN1--CXXC5"
+)
+embryGenes = c(
+  "FOXR2",
+  "MN1",
+  "TTYH1"
+)
+
+#' Generate filtered fusion frame
+#' @param df Unfiltered fusion data frame
+#' @param bioid List of biospecimen IDs
+#' @param fuses List of explicit fusion names
+#' @param genes List of gene names
+#' @return the filtered fusion data frame
+filterFusion <- function(df, bioid, fuses, genes) {
+  if (!missing(bioid)) {
+    df <- filter(df, Sample %in% bioid)
+  }
+  if (!missing(fuses) & !missing(genes)) {
+    df <- filter(df, FusionName %in% fuses | 
+                   Gene1A %in% genes |
+                   Gene2A %in% genes |
+                   Gene1B %in% genes |
+                   Gene2B %in% genes)
+  } else if (!missing(fuses)) {
+    df <- filter(df, FusionName %in% fuses)
+  } else if (!missing(genes)) {
+    df <- filter(df,     
+                 Gene1A %in% genes |
+                   Gene2A %in% genes |
+                   Gene1B %in% genes |
+                   Gene2B %in% genes)
+  }
+  return(df)
+}
+
+#' Creates a TSV of the filtered fusion sheet
+#' @param df The filtered fusion data frame
+#' @param fuses List of explicit fusion names
+#' @param outputPath Path of the output file
+#' @return Writes a TSV to the output path
+generateOutput <- function(df, fuses, outputPath) {
+  # create a list to be used to reduce the table to its minimal set
+  # minimal set is the explicit fusions + any other non-specific fusions in the table
+  lvls = unique(c(fuses, sort(as.character(unique(df$FusionName)))))
+  df$FusionName = factor(df$FusionName, levels=lvls)
+  # convert the table to a table dropping the empty levels
+  tbl = table(droplevels(df)$Sample,df$FusionName)
+  # convert back to a matrix
+  mtx = as.data.frame.matrix(tbl)
+  # convert the rownames into the first row
+  mtx = setDT(mtx,keep.rownames=TRUE)
+  # add in a column name for the rownames
+  colnames(mtx) = c("Kids_First_Biospecimen_ID",lvls)
+  write.table(mtx, file=outputPath, sep="\t", quote=FALSE, row.names=FALSE)
+}
+
+#' Set up the options
+optionList <- list(
+  make_option(
+    opt_str = c("-d","--demographic_file"), type = "character",
+    default = NULL, help = "Path to the demographic file."
+  ),
+  make_option(
+    opt_str = c("-f","--fusions_file"), type = "character",
+    default = NULL, help = "Path to the fusions file."
+  ),
+  make_option(
+    opt_str = c("-o", "--output_dir"), type = "character",
+    default = "pbta-consolidated-fusions", help = "Output directory for output files."
+  )
+)
+
+#' Parse the options
+opt <- parse_args(OptionParser(option_list = optionList))
+
+#' Check the output directory
+if (!dir.exists(opt$output_dir)) {
+  dir.create(opt$output_dir)
+}
+
+#' Check that the files exist
+if (!file.exists(opt$demographic_file)) {
+  demo_missing <- paste("Error:", opt$demographic_file, "does not exist")
+  if (!file.exists(opt$fusions_file)) {
+    stop(paste(demo_missing, "\nError:", opt$fusions_file, "does not exist"))
+  } else
+    stop(demo_missing)
+} else if (!file.exists(opt$fusions_file)) {
+  stop(paste("Error:", opt$fusions_file, "does not exist"))
+}
+#' Load the files
+demo <- read.csv(opt$demographic_file, sep="\t")
+fuse <- read.csv(opt$fusions_file, sep="\t")
+
+#' Use the filters from above to get the biospecimen ids
+demoEpend.bios <- filter(demo,
+                        short_histology == ependSH)$Kids_First_Biospecimen_ID
+demoEmbry.bios <- filter(demo,
+                        broad_histology == embryBH &
+                          !(short_histology %in% embrySH))$Kids_First_Biospecimen_ID
+
+#' Filter the fusion files for your two populations
+fuseEpend <- filterFusion(df = fuse, 
+                          bioid = demoEpend.bios, 
+                          fuses = ependFuses)
+fuseEmbry <- filterFusion(df = fuse, 
+                          bioid = demoEmbry.bios, 
+                          fuses = embryFuses, 
+                          genes = embryGenes)
+#' Write the fusion frames to file
+generateOutput(df = fuseEpend, 
+               fuses = ependFuses, 
+               outputPath = file.path(
+                 opt$output_dir,"ependymoma_fusion_summary.tsv"))
+generateOutput(df = fuseEmbry,
+               fuses = embryFuses,
+               outputPath = file.path(
+                 opt$output_dir,"embryomal_fusion_summary.tsv"))
diff --git a/analyses/fusion-summary/README.md b/analyses/fusion-summary/README.md
new file mode 100644
index 0000000000..26218cf940
--- /dev/null
+++ b/analyses/fusion-summary/README.md
@@ -0,0 +1,19 @@
+# Fusion Summary
+
+This module generates summary files for fusions of interest present in biospecimens taken from:
+1. Ependymoma tumors
+2. Embryonal tumors not from ATRT or MB
+
+To genereate the tables simply run:
+```
+./run-new-analysis.sh
+```
+
+## General Use
+
+The program generates files that contain information about the presence or absence of specific fusions or genes participating in fusions.
+These can be potentially used for further downstream molecular subtyping analyses.
+
+### Reference
+
+https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398
diff --git a/analyses/fusion-summary/results/embryomal_fusion_summary.tsv b/analyses/fusion-summary/results/embryomal_fusion_summary.tsv
new file mode 100644
index 0000000000..61debb2e50
--- /dev/null
+++ b/analyses/fusion-summary/results/embryomal_fusion_summary.tsv
@@ -0,0 +1,2 @@
+Kids_First_Biospecimen_ID	CIC--NUTM1	MN1--BEND2	MN1--CXXC5	TTYH1--MIR512-2/MIR1323	TTYH1--MIR515-2/MIR519C
+BS_37GTVG4N	0	0	0	1	1
diff --git a/analyses/fusion-summary/results/ependymoma_fusion_summary.tsv b/analyses/fusion-summary/results/ependymoma_fusion_summary.tsv
new file mode 100644
index 0000000000..3a7a9bb394
--- /dev/null
+++ b/analyses/fusion-summary/results/ependymoma_fusion_summary.tsv
@@ -0,0 +1,31 @@
+Kids_First_Biospecimen_ID	C11orf95--MAML2	C11orf95--RELA	C11orf95--YAP1	LTBP3--RELA	PTEN--TAS2R1	YAP1--FAM118B	YAP1--MAMLD1	YAP1--MAMLD2
+BS_07ANYSYQ	0	1	0	0	0	0	0	0
+BS_0WQJP6ZG	0	1	0	0	0	0	0	0
+BS_0XEG6SNV	0	1	0	0	0	0	0	0
+BS_4NWHYH53	0	1	0	0	0	0	0	0
+BS_6MZ7FRZH	0	1	0	0	0	0	0	0
+BS_7G42J2SK	0	1	0	0	0	0	0	0
+BS_C05FKR8X	0	1	0	0	0	0	0	0
+BS_CXVJK2FY	0	1	0	0	0	0	0	0
+BS_CZ3ER8DY	0	1	0	0	0	0	0	0
+BS_CZ3NA7KV	0	1	0	0	0	0	0	0
+BS_EK5PCKY0	0	1	0	0	0	0	0	0
+BS_FTKPQ5FZ	0	1	0	0	0	0	0	0
+BS_FW5ECXXK	0	1	0	0	0	0	0	0
+BS_G23JJAZY	0	1	0	0	0	0	0	0
+BS_G63HYD6N	0	1	0	0	0	0	0	0
+BS_H4NXBD2D	0	1	0	0	0	0	0	0
+BS_J70GK8SM	1	0	0	0	0	0	0	0
+BS_KBT7MQ6H	0	2	0	0	0	0	0	0
+BS_MT15SGJN	0	1	0	0	0	0	0	0
+BS_N5DVEJXT	0	1	0	0	0	0	0	0
+BS_NB42PWZN	0	1	0	0	0	0	0	0
+BS_NGHK9RZP	0	1	0	0	0	0	0	0
+BS_QSTAVWGE	0	1	0	0	0	0	0	0
+BS_QXKRN6CR	0	1	0	0	0	0	0	0
+BS_T1DVKKJB	0	1	0	0	0	0	0	0
+BS_V4W81SFC	0	0	0	0	0	0	1	0
+BS_VAAHBH60	0	1	0	0	0	0	0	0
+BS_W80TJC27	0	1	0	0	0	0	0	0
+BS_XF0ZX2B3	0	1	0	0	0	0	0	0
+BS_Z7890YNR	0	1	0	0	0	0	0	0
diff --git a/analyses/fusion-summary/run-new-analysis.sh b/analyses/fusion-summary/run-new-analysis.sh
new file mode 100644
index 0000000000..f8b71d616e
--- /dev/null
+++ b/analyses/fusion-summary/run-new-analysis.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -e
+set -o pipefail
+
+# This script should always run as if it were being called from
+# the directory it lives in.
+script_directory="$(perl -e 'use File::Basename;
+  use Cwd "abs_path";
+  print dirname(abs_path(@ARGV[0]));' -- "$0")"
+cd "$script_directory" || exit
+
+data_dir="../../data"
+scratch_dir="../..scratch"
+
+demographic_file="${data_dir}/pbta-histologies.tsv"
+fusions_file="${data_dir}/pbta-fusion-putative-oncogenic.tsv"
+
+Rscript --vanilla ${script_directory}/01-fusion-summary.R \
+  --demographic_file ${demographic_file} \
+  --fusions_file ${fusions_file} \
+  --output_dir ${script_directory}/results 

From 95994d49a899f9c71ea30d27db254b28e96a9131 Mon Sep 17 00:00:00 2001
From: Dan Miller <dmiller5191@gmail.com>
Date: Wed, 8 Jan 2020 14:16:17 +0000
Subject: [PATCH 2/5] added files without biospecimen filter

---
 analyses/fusion-summary/01-fusion-summary.R   | 13 +++++++
 .../results/fusion_summary_embryonal_foi.tsv  | 12 ++++++
 .../results/fusion_summary_ependymoma_foi.tsv | 37 +++++++++++++++++++
 3 files changed, 62 insertions(+)
 create mode 100644 analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
 create mode 100644 analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv

diff --git a/analyses/fusion-summary/01-fusion-summary.R b/analyses/fusion-summary/01-fusion-summary.R
index 05f40e9453..6a90662414 100644
--- a/analyses/fusion-summary/01-fusion-summary.R
+++ b/analyses/fusion-summary/01-fusion-summary.R
@@ -143,7 +143,20 @@ fuseEmbry <- filterFusion(df = fuse,
                           bioid = demoEmbry.bios, 
                           fuses = embryFuses, 
                           genes = embryGenes)
+allFuseEpend <- filterFusion(df = fuse,
+                          fuses = ependFuses)
+allFuseEmbry <- filterFusion(df = fuse,
+                          fuses = embryFuses,
+                          genes = embryGenes)
 #' Write the fusion frames to file
+generateOutput(df  = allFuseEpend,
+               fuses = ependFuses,
+               outputPath = file.path(
+                 opt$output_dir,"fusion_summary_ependymoma_foi.tsv"))
+generateOutput(df = allFuseEmbry,
+               fuses = embryFuses,
+               outputPath = file.path(
+                 opt$output_dir,"fusion_summary_embryonal_foi.tsv"))
 generateOutput(df = fuseEpend, 
                fuses = ependFuses, 
                outputPath = file.path(
diff --git a/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv b/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
new file mode 100644
index 0000000000..4fb610a288
--- /dev/null
+++ b/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
@@ -0,0 +1,12 @@
+Kids_First_Biospecimen_ID	CIC--NUTM1	MN1--BEND2	MN1--CXXC5	MACF1--TTYH1	MN1--AC008667.1	MN1--PATZ1	MN1--PSD2	NPAS3--AC245884.4/TTYH1	TTYH1--DPRX/RNU6-698P	TTYH1--MIR512-2/MIR1323	TTYH1--MIR515-2/MIR519C	ZC4H2--AL627224.1/FOXR2	ZC4H2--FOXR2
+BS_37GTVG4N	0	0	0	0	0	0	0	0	0	1	1	0	0
+BS_65VFS9N1	0	0	0	0	0	0	0	0	1	0	0	0	0
+BS_685DACMS	0	0	0	0	0	0	0	0	1	0	0	0	0
+BS_HWGWYCY7	0	0	0	0	0	0	0	1	0	0	0	0	0
+BS_KSKZ9J7J	0	0	2	0	1	0	1	0	0	0	0	0	0
+BS_N6N147BY	0	0	0	0	0	0	0	0	1	0	0	0	0
+BS_P39SQPTS	0	0	0	0	0	0	0	0	0	1	0	0	0
+BS_QWNBZ9RJ	0	0	0	0	0	0	0	0	1	0	0	0	0
+BS_S5P8VTN5	0	0	0	1	0	0	0	0	0	0	0	0	0
+BS_YBJBSRHV	0	0	0	0	0	0	0	0	0	0	0	1	1
+BS_ZVZDDW2G	0	0	0	0	0	2	0	0	0	0	0	0	0
diff --git a/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv b/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv
new file mode 100644
index 0000000000..0dfa618995
--- /dev/null
+++ b/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv
@@ -0,0 +1,37 @@
+Kids_First_Biospecimen_ID	C11orf95--MAML2	C11orf95--RELA	C11orf95--YAP1	LTBP3--RELA	PTEN--TAS2R1	YAP1--FAM118B	YAP1--MAMLD1	YAP1--MAMLD2
+BS_07ANYSYQ	0	1	0	0	0	0	0	0
+BS_0WQJP6ZG	0	1	0	0	0	0	0	0
+BS_0XEG6SNV	0	1	0	0	0	0	0	0
+BS_23M72ABG	0	0	0	0	0	2	0	0
+BS_4NWHYH53	0	1	0	0	0	0	0	0
+BS_6MZ7FRZH	0	1	0	0	0	0	0	0
+BS_7G42J2SK	0	1	0	0	0	0	0	0
+BS_C05FKR8X	0	1	0	0	0	0	0	0
+BS_CXVJK2FY	0	1	0	0	0	0	0	0
+BS_CZ3ER8DY	0	1	0	0	0	0	0	0
+BS_CZ3NA7KV	0	1	0	0	0	0	0	0
+BS_D9GEXXHX	0	0	0	0	0	1	0	0
+BS_EK5PCKY0	0	1	0	0	0	0	0	0
+BS_FTKPQ5FZ	0	1	0	0	0	0	0	0
+BS_FW5ECXXK	0	1	0	0	0	0	0	0
+BS_G23JJAZY	0	1	0	0	0	0	0	0
+BS_G63HYD6N	0	1	0	0	0	0	0	0
+BS_H4NXBD2D	0	1	0	0	0	0	0	0
+BS_J70GK8SM	1	0	0	0	0	0	0	0
+BS_KBT7MQ6H	0	2	0	0	0	0	0	0
+BS_KR4MP5ET	0	0	0	0	0	2	0	0
+BS_MQCKXD60	0	1	0	0	0	0	0	0
+BS_MT15SGJN	0	1	0	0	0	0	0	0
+BS_N5DVEJXT	0	1	0	0	0	0	0	0
+BS_NB42PWZN	0	1	0	0	0	0	0	0
+BS_NGHK9RZP	0	1	0	0	0	0	0	0
+BS_PN2CE34A	0	0	0	0	0	1	0	0
+BS_QSTAVWGE	0	1	0	0	0	0	0	0
+BS_QXKRN6CR	0	1	0	0	0	0	0	0
+BS_SXCZ3CXN	0	1	0	0	0	0	0	0
+BS_T1DVKKJB	0	1	0	0	0	0	0	0
+BS_V4W81SFC	0	0	0	0	0	0	1	0
+BS_VAAHBH60	0	1	0	0	0	0	0	0
+BS_W80TJC27	0	1	0	0	0	0	0	0
+BS_XF0ZX2B3	0	1	0	0	0	0	0	0
+BS_Z7890YNR	0	1	0	0	0	0	0	0

From 0a2729d451e3128d10ef790b4c6cb6a1f32012d2 Mon Sep 17 00:00:00 2001
From: Dan Miller <dmiller5191@gmail.com>
Date: Wed, 8 Jan 2020 18:06:25 +0000
Subject: [PATCH 3/5] change relabel of column names

---
 analyses/fusion-summary/01-fusion-summary.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/analyses/fusion-summary/01-fusion-summary.R b/analyses/fusion-summary/01-fusion-summary.R
index 6a90662414..d993cadaa8 100644
--- a/analyses/fusion-summary/01-fusion-summary.R
+++ b/analyses/fusion-summary/01-fusion-summary.R
@@ -85,8 +85,8 @@ generateOutput <- function(df, fuses, outputPath) {
   mtx = as.data.frame.matrix(tbl)
   # convert the rownames into the first row
   mtx = setDT(mtx,keep.rownames=TRUE)
-  # add in a column name for the rownames
-  colnames(mtx) = c("Kids_First_Biospecimen_ID",lvls)
+  # rename the column of the rownames
+  colnames(mtx)[colnames(mtx) == 'rn'] <- 'Kids_First_Biospecimen_ID'
   write.table(mtx, file=outputPath, sep="\t", quote=FALSE, row.names=FALSE)
 }
 

From 69b45682d5ac56ad6452c7987d50a169cdd61184 Mon Sep 17 00:00:00 2001
From: Dan Miller <dmiller5191@gmail.com>
Date: Thu, 9 Jan 2020 15:10:34 +0000
Subject: [PATCH 4/5] removed demographic filtering added RELA gene filtering
 no longer drop levels of samples

---
 analyses/fusion-summary/01-fusion-summary.R   |  40 +-
 .../results/embryomal_fusion_summary.tsv      |   2 -
 .../results/ependymoma_fusion_summary.tsv     |  31 -
 .../results/fusion_summary_embryonal_foi.tsv  | 776 ++++++++++++++++
 .../results/fusion_summary_ependymoma_foi.tsv | 825 +++++++++++++++++-
 5 files changed, 1571 insertions(+), 103 deletions(-)
 delete mode 100644 analyses/fusion-summary/results/embryomal_fusion_summary.tsv
 delete mode 100644 analyses/fusion-summary/results/ependymoma_fusion_summary.tsv

diff --git a/analyses/fusion-summary/01-fusion-summary.R b/analyses/fusion-summary/01-fusion-summary.R
index d993cadaa8..950a8bc346 100644
--- a/analyses/fusion-summary/01-fusion-summary.R
+++ b/analyses/fusion-summary/01-fusion-summary.R
@@ -8,14 +8,6 @@ suppressPackageStartupMessages(library("optparse"))
 
 #' **Filters**
 #' 
-#' *Demographic Filers*
-#' 1: Used to filter short_histology to get Ependymoma tumors 
-ependSH = "Ependymoma"
-#' 2: Used for Embryonal tumors (short_histology)
-#'  not from ATRT or MB (broad_histology)
-embryBH = "Embryonal tumor"
-embrySH = c("ATRT", "Medulloblastoma")
-#' 
 #' *Fusions Filters*
 #' 1: Exact match a list of fusions common in Ependymoma tumors
 ependFuses = c(
@@ -28,6 +20,9 @@ ependFuses = c(
   "YAP1--MAMLD1",
   "YAP1--MAMLD2"
 )
+ependGenes = c(
+  "RELA"
+)
 #' 2: Exact match a list of fusions common in Embryonal tumors
 #' as well as fusions containing a particular gene with any other gene
 embryFuses = c(
@@ -79,8 +74,8 @@ generateOutput <- function(df, fuses, outputPath) {
   # minimal set is the explicit fusions + any other non-specific fusions in the table
   lvls = unique(c(fuses, sort(as.character(unique(df$FusionName)))))
   df$FusionName = factor(df$FusionName, levels=lvls)
-  # convert the table to a table dropping the empty levels
-  tbl = table(droplevels(df)$Sample,df$FusionName)
+  # convert the data frame to a table
+  tbl = table(df$Sample,df$FusionName)
   # convert back to a matrix
   mtx = as.data.frame.matrix(tbl)
   # convert the rownames into the first row
@@ -128,23 +123,10 @@ if (!file.exists(opt$demographic_file)) {
 demo <- read.csv(opt$demographic_file, sep="\t")
 fuse <- read.csv(opt$fusions_file, sep="\t")
 
-#' Use the filters from above to get the biospecimen ids
-demoEpend.bios <- filter(demo,
-                        short_histology == ependSH)$Kids_First_Biospecimen_ID
-demoEmbry.bios <- filter(demo,
-                        broad_histology == embryBH &
-                          !(short_histology %in% embrySH))$Kids_First_Biospecimen_ID
-
 #' Filter the fusion files for your two populations
-fuseEpend <- filterFusion(df = fuse, 
-                          bioid = demoEpend.bios, 
-                          fuses = ependFuses)
-fuseEmbry <- filterFusion(df = fuse, 
-                          bioid = demoEmbry.bios, 
-                          fuses = embryFuses, 
-                          genes = embryGenes)
 allFuseEpend <- filterFusion(df = fuse,
-                          fuses = ependFuses)
+                          fuses = ependFuses,
+                          genes = ependGenes)
 allFuseEmbry <- filterFusion(df = fuse,
                           fuses = embryFuses,
                           genes = embryGenes)
@@ -157,11 +139,3 @@ generateOutput(df = allFuseEmbry,
                fuses = embryFuses,
                outputPath = file.path(
                  opt$output_dir,"fusion_summary_embryonal_foi.tsv"))
-generateOutput(df = fuseEpend, 
-               fuses = ependFuses, 
-               outputPath = file.path(
-                 opt$output_dir,"ependymoma_fusion_summary.tsv"))
-generateOutput(df = fuseEmbry,
-               fuses = embryFuses,
-               outputPath = file.path(
-                 opt$output_dir,"embryomal_fusion_summary.tsv"))
diff --git a/analyses/fusion-summary/results/embryomal_fusion_summary.tsv b/analyses/fusion-summary/results/embryomal_fusion_summary.tsv
deleted file mode 100644
index 61debb2e50..0000000000
--- a/analyses/fusion-summary/results/embryomal_fusion_summary.tsv
+++ /dev/null
@@ -1,2 +0,0 @@
-Kids_First_Biospecimen_ID	CIC--NUTM1	MN1--BEND2	MN1--CXXC5	TTYH1--MIR512-2/MIR1323	TTYH1--MIR515-2/MIR519C
-BS_37GTVG4N	0	0	0	1	1
diff --git a/analyses/fusion-summary/results/ependymoma_fusion_summary.tsv b/analyses/fusion-summary/results/ependymoma_fusion_summary.tsv
deleted file mode 100644
index 3a7a9bb394..0000000000
--- a/analyses/fusion-summary/results/ependymoma_fusion_summary.tsv
+++ /dev/null
@@ -1,31 +0,0 @@
-Kids_First_Biospecimen_ID	C11orf95--MAML2	C11orf95--RELA	C11orf95--YAP1	LTBP3--RELA	PTEN--TAS2R1	YAP1--FAM118B	YAP1--MAMLD1	YAP1--MAMLD2
-BS_07ANYSYQ	0	1	0	0	0	0	0	0
-BS_0WQJP6ZG	0	1	0	0	0	0	0	0
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-BS_NGHK9RZP	0	1	0	0	0	0	0	0
-BS_QSTAVWGE	0	1	0	0	0	0	0	0
-BS_QXKRN6CR	0	1	0	0	0	0	0	0
-BS_T1DVKKJB	0	1	0	0	0	0	0	0
-BS_V4W81SFC	0	0	0	0	0	0	1	0
-BS_VAAHBH60	0	1	0	0	0	0	0	0
-BS_W80TJC27	0	1	0	0	0	0	0	0
-BS_XF0ZX2B3	0	1	0	0	0	0	0	0
-BS_Z7890YNR	0	1	0	0	0	0	0	0
diff --git a/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv b/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
index 4fb610a288..1dc40bc1bc 100644
--- a/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
+++ b/analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
@@ -1,12 +1,788 @@
 Kids_First_Biospecimen_ID	CIC--NUTM1	MN1--BEND2	MN1--CXXC5	MACF1--TTYH1	MN1--AC008667.1	MN1--PATZ1	MN1--PSD2	NPAS3--AC245884.4/TTYH1	TTYH1--DPRX/RNU6-698P	TTYH1--MIR512-2/MIR1323	TTYH1--MIR515-2/MIR519C	ZC4H2--AL627224.1/FOXR2	ZC4H2--FOXR2
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 BS_ZVZDDW2G	0	0	0	0	0	2	0	0	0	0	0	0	0
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diff --git a/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv b/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv
index 0dfa618995..295c1c80d4 100644
--- a/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv
+++ b/analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv
@@ -1,37 +1,788 @@
-Kids_First_Biospecimen_ID	C11orf95--MAML2	C11orf95--RELA	C11orf95--YAP1	LTBP3--RELA	PTEN--TAS2R1	YAP1--FAM118B	YAP1--MAMLD1	YAP1--MAMLD2
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-BS_0XEG6SNV	0	1	0	0	0	0	0	0
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From bba4e786b38a3cac4b3cf1e32796b8b9170d81f1 Mon Sep 17 00:00:00 2001
From: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date: Thu, 9 Jan 2020 12:20:25 -0500
Subject: [PATCH 5/5] No longer need demographic file

---
 analyses/fusion-summary/01-fusion-summary.R | 32 +++++++--------------
 analyses/fusion-summary/run-new-analysis.sh |  4 +--
 2 files changed, 11 insertions(+), 25 deletions(-)

diff --git a/analyses/fusion-summary/01-fusion-summary.R b/analyses/fusion-summary/01-fusion-summary.R
index 950a8bc346..3ceaafd0f7 100644
--- a/analyses/fusion-summary/01-fusion-summary.R
+++ b/analyses/fusion-summary/01-fusion-summary.R
@@ -7,13 +7,13 @@ suppressPackageStartupMessages(library("data.table"))
 suppressPackageStartupMessages(library("optparse"))
 
 #' **Filters**
-#' 
+#'
 #' *Fusions Filters*
 #' 1: Exact match a list of fusions common in Ependymoma tumors
 ependFuses = c(
   "C11orf95--MAML2",
   "C11orf95--RELA",
-  "C11orf95--YAP1", 
+  "C11orf95--YAP1",
   "LTBP3--RELA",
   "PTEN--TAS2R1",
   "YAP1--FAM118B",
@@ -47,7 +47,7 @@ filterFusion <- function(df, bioid, fuses, genes) {
     df <- filter(df, Sample %in% bioid)
   }
   if (!missing(fuses) & !missing(genes)) {
-    df <- filter(df, FusionName %in% fuses | 
+    df <- filter(df, FusionName %in% fuses |
                    Gene1A %in% genes |
                    Gene2A %in% genes |
                    Gene1B %in% genes |
@@ -55,7 +55,7 @@ filterFusion <- function(df, bioid, fuses, genes) {
   } else if (!missing(fuses)) {
     df <- filter(df, FusionName %in% fuses)
   } else if (!missing(genes)) {
-    df <- filter(df,     
+    df <- filter(df,
                  Gene1A %in% genes |
                    Gene2A %in% genes |
                    Gene1B %in% genes |
@@ -87,10 +87,6 @@ generateOutput <- function(df, fuses, outputPath) {
 
 #' Set up the options
 optionList <- list(
-  make_option(
-    opt_str = c("-d","--demographic_file"), type = "character",
-    default = NULL, help = "Path to the demographic file."
-  ),
   make_option(
     opt_str = c("-f","--fusions_file"), type = "character",
     default = NULL, help = "Path to the fusions file."
@@ -109,27 +105,19 @@ if (!dir.exists(opt$output_dir)) {
   dir.create(opt$output_dir)
 }
 
-#' Check that the files exist
-if (!file.exists(opt$demographic_file)) {
-  demo_missing <- paste("Error:", opt$demographic_file, "does not exist")
-  if (!file.exists(opt$fusions_file)) {
-    stop(paste(demo_missing, "\nError:", opt$fusions_file, "does not exist"))
-  } else
-    stop(demo_missing)
-} else if (!file.exists(opt$fusions_file)) {
+if (!file.exists(opt$fusions_file))
   stop(paste("Error:", opt$fusions_file, "does not exist"))
-}
+
 #' Load the files
-demo <- read.csv(opt$demographic_file, sep="\t")
 fuse <- read.csv(opt$fusions_file, sep="\t")
 
 #' Filter the fusion files for your two populations
 allFuseEpend <- filterFusion(df = fuse,
-                          fuses = ependFuses,
-                          genes = ependGenes)
+                             fuses = ependFuses,
+                             genes = ependGenes)
 allFuseEmbry <- filterFusion(df = fuse,
-                          fuses = embryFuses,
-                          genes = embryGenes)
+                             fuses = embryFuses,
+                             genes = embryGenes)
 #' Write the fusion frames to file
 generateOutput(df  = allFuseEpend,
                fuses = ependFuses,
diff --git a/analyses/fusion-summary/run-new-analysis.sh b/analyses/fusion-summary/run-new-analysis.sh
index f8b71d616e..4cfea1e932 100644
--- a/analyses/fusion-summary/run-new-analysis.sh
+++ b/analyses/fusion-summary/run-new-analysis.sh
@@ -13,10 +13,8 @@ cd "$script_directory" || exit
 data_dir="../../data"
 scratch_dir="../..scratch"
 
-demographic_file="${data_dir}/pbta-histologies.tsv"
 fusions_file="${data_dir}/pbta-fusion-putative-oncogenic.tsv"
 
 Rscript --vanilla ${script_directory}/01-fusion-summary.R \
-  --demographic_file ${demographic_file} \
   --fusions_file ${fusions_file} \
-  --output_dir ${script_directory}/results 
+  --output_dir ${script_directory}/results