update subset files for lgat fusions (#835)

Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
AlexsLemonade · Nov 12, 2020 · ff2ce76 · ff2ce76
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diff --git a/analyses/create-subset-files/02-subset_files.R b/analyses/create-subset-files/02-subset_files.R
@@ -109,7 +109,7 @@ subset_files <- function(filename, biospecimen_ids, output_directory) {
       fusion_file %>%
         dplyr::filter(Sample %in% biospecimen_ids |
                         # this is required for the the fusion-summary module
-                        grepl("RELA|MN1|EWSR1", FusionName)) %>%
+                        grepl("RELA|MN1|EWSR1|FGFR1--TACC1|MYB--QKI|BRAF", FusionName)) %>%
         readr::write_tsv(output_file)
     } else if (grepl("bysample", filename)) {
       fusion_file %>%

diff --git a/analyses/create-subset-files/README.md b/analyses/create-subset-files/README.md
@@ -29,7 +29,7 @@ Certain analysis modules have required modifications to the subset file creation
 * [`sex-prediction-from-RNASeq`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sex-prediction-from-RNASeq) required that we specified `Male` and `Female` samples (`reported_gender`) were both represented in the `stranded` RNA-seq data.
 * `tp53_nf1_module` requires us to include a set of biospecimen IDs for samples that have _TP53_ and _NF1_ mutations and are present in the `stranded` RNA-seq dataset.
 See the `00-enrich-positive-examples` notebook for more information.
-* `fusion-summary` requires us to include fusions that involve _MN1_, _RELA_, or _EWSR1_.
+* `fusion-summary` requires us to include _FGFR1--TACC1_, _MYB--QKI_, fusions or fusions that involve _BRAF_, _MN1_, _RELA_, or _EWSR1_.
 
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