fusions_ided.Rmd

---
title: "Gene overexpression Fusions identified"
output: html_notebook
---
#list of packages used
```{r}
library(readr)
```


#list of fusions ided by outliers
```{r}
outlier_fusions <- all_genes %>% filter(fusion == "Fusion", is_outlier == TRUE) %>% group_by(gene, Cancer) %>% select(rail_id, gene, Project_ID)
outlier_fusions
write_csv(outlier_fusions, "outlier_fusions.csv")
```

#list of fusions ided by overexpression (95th percentile)
```{r}
above_95percent <- all_genes %>% filter(fusion == "Fusion", above_95 == TRUE) %>% group_by(gene, Cancer) %>% select(rail_id, gene, Project_ID)]
above_95percent
write_csv(above_95percent, "above_95percent.csv")
```

#list of fusions ided by both methods
```{r}
ided_by_both <- all_genes %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion == "Fusion") %>% select(rail_id, gene, Project_ID)
ided_by_both
write_csv(ided_by_both, 'ided_by_both.csv')
```

##false positives (only cancer types with fusions)
#overexpression
```{r}
t <- tacc3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "ESCA" | Project_ID == "GBM" | Project_ID == "HNSC" | Project_ID == "KIRP" | Project_ID == "LAML" | Project_ID == "LGG" | Project_ID == "LIHC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

al <- alk_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "KIRP" | Project_ID == "LUAD" | Project_ID == "READ" | Project_ID == "SARC" | Project_ID == "SKCM" | Project_ID == "THCA") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

ar <- arhgap26_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "CESC" | Project_ID == "HNSC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "SARC" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

er <- erg_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "CESC" | Project_ID == "LGG" | Project_ID == "PAAD" | Project_ID == "PCPG" | Project_ID == "PRAD") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

et <- etv1_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "LGG" | Project_ID == "PRAD") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

m <- maml3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "LIHC" | Project_ID == "PCPG") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

n <- ntrk3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "COAD" | Project_ID == "HNSC" | Project_ID == "LGG" | Project_ID == "PAAD" | Project_ID == "SKCM" | Project_ID == "THCA") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

ra <- rara_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "GBM" | Project_ID == "LAML" | Project_ID == "OV" | Project_ID == "PCPG" | Project_ID == "READ" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

re <- ret_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "COAD" | Project_ID == "LAML" | Project_ID == "LUAD" | Project_ID == "OV" | Project_ID == "THCA") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

tf <- tfe3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "KIRC" | Project_ID == "KIRP" | Project_ID == "UCEC") %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

fpr_specific <- rbind(al, ar, er, et, m, n, ra, re, t, tf)
fpr_specific <- fpr_specific %>% .[order(.$gene, .$Project_ID),]
fpr_specific
write_csv(fpr_specific, 'overexp_fpr_specific.csv')
```
#outliers
```{r}
t <- tacc3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "ESCA" | Project_ID == "GBM" | Project_ID == "HNSC" | Project_ID == "KIRP" | Project_ID == "LAML" | Project_ID == "LGG" | Project_ID == "LIHC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "STAD") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

al <- alk_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "KIRP" | Project_ID == "LUAD" | Project_ID == "READ" | Project_ID == "SARC" | Project_ID == "SKCM" | Project_ID == "THCA") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

ar <- arhgap26_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "CESC" | Project_ID == "HNSC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "SARC" | Project_ID == "STAD") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

er <- erg_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "CESC" | Project_ID == "LGG" | Project_ID == "PAAD" | Project_ID == "PCPG" | Project_ID == "PRAD") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

et <- etv1_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "LGG" | Project_ID == "PRAD") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

m <- maml3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "LIHC" | Project_ID == "PCPG") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

n <- ntrk3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "COAD" | Project_ID == "HNSC" | Project_ID == "LGG" | Project_ID == "PAAD" | Project_ID == "SKCM" | Project_ID == "THCA") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

ra <- rara_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "GBM" | Project_ID == "LAML" | Project_ID == "OV" | Project_ID == "PCPG" | Project_ID == "READ" | Project_ID == "STAD") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

re <- ret_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "COAD" | Project_ID == "LAML" | Project_ID == "LUAD" | Project_ID == "OV" | Project_ID == "THCA") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

tf <- tfe3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "KIRC" | Project_ID == "KIRP" | Project_ID == "UCEC") %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

fpr_specific_outlier <- rbind(al, ar, er, et, m, n, ra, re, t, tf)
fpr_specific_outlier <- fpr_specific_outlier %>% .[order(.$gene, .$Project_ID),]
fpr_specific_outlier
write_csv(fpr_specific_outlier, 'fpr_specific_outlier.csv')
```

#shared
```{r}
t <- tacc3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "ESCA" | Project_ID == "GBM" | Project_ID == "HNSC" | Project_ID == "KIRP" | Project_ID == "LAML" | Project_ID == "LGG" | Project_ID == "LIHC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

al <- alk_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "KIRP" | Project_ID == "LUAD" | Project_ID == "READ" | Project_ID == "SARC" | Project_ID == "SKCM" | Project_ID == "THCA") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

ar <- arhgap26_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "CESC" | Project_ID == "HNSC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "SARC" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

er <- erg_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "CESC" | Project_ID == "LGG" | Project_ID == "PAAD" | Project_ID == "PCPG" | Project_ID == "PRAD") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

et <- etv1_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "LGG" | Project_ID == "PRAD") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

m <- maml3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "LIHC" | Project_ID == "PCPG") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

n <- ntrk3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "COAD" | Project_ID == "HNSC" | Project_ID == "LGG" | Project_ID == "PAAD" | Project_ID == "SKCM" | Project_ID == "THCA") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

ra <- rara_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "GBM" | Project_ID == "LAML" | Project_ID == "OV" | Project_ID == "PCPG" | Project_ID == "READ" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

re <- ret_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BRCA" | Project_ID == "COAD" | Project_ID == "LAML" | Project_ID == "LUAD" | Project_ID == "OV" | Project_ID == "THCA") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

tf <- tfe3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "KIRC" | Project_ID == "KIRP" | Project_ID == "UCEC") %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% 
  select(rail_id, gene, Project_ID)

fpr_specific_shared <- rbind(al, ar, er, et, m, n, ra, re, t, tf)
fpr_specific_shared <- fpr_specific_shared %>% .[order(.$gene, .$Project_ID),]
fpr_specific_shared
write_csv(fpr_specific_shared, 'fpr_specific_shared.csv')
```

#total false positives (including all cancers)
```{r}
outlier_false_pos <- all_genes %>%
  filter(is_outlier == TRUE, fusion != "Fusion") %>% select(rail_id, gene, Project_ID)
write_csv(outlier_false_pos, 'outlier_false_pos.csv')

above95_false_pos <- all_genes %>%
  filter(above_95 == TRUE, fusion != "Fusion") %>% select(rail_id, gene, Project_ID)
write_csv(above95_false_pos, 'above95_false_pos.csv')

shared_false_pos <- all_genes %>%
  filter(above_95 == TRUE, is_outlier == TRUE, fusion != "Fusion") %>% select(rail_id, gene, Project_ID)
write_csv(shared_false_pos, 'shared_false_pos.csv')
```
```{r}
tacc3_combined %>% filter(has_cancer != "GTEx", above_95 == TRUE)
all_genes %>%
  filter(has_cancer == "Cancer", above_95 == TRUE, fusion != "Fusion") %>% select(rail_id, gene, Project_ID) %>% distinct(rail_id)
above95_false_pos %>% filter(has_cancer == "Cancer") %>% distinct(rail_id)
```

```{r}
tacc3_combined %>% filter(has_cancer == "Cancer", fusion != "Fusion") %>% filter(Project_ID == "BLCA" | Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "ESCA" | Project_ID == "GBM" | Project_ID == "HNSC" | Project_ID == "KIRP" | Project_ID == "LAML" | Project_ID == "LGG" | Project_ID == "LIHC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "STAD") %>% ungroup() %>% group_by(Project_ID) %>% distinct(rail_id) %>% summarise(n())
```
```{r}
tacc3_combined %>% filter(has_cancer != "GTEx", fusion != "Fusion") %>% filter(Project_ID == "BLCA" | Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "ESCA" | Project_ID == "GBM" | Project_ID == "HNSC" | Project_ID == "KIRP" | Project_ID == "LAML" | Project_ID == "LGG" | Project_ID == "LIHC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "STAD") %>% ungroup() %>% summarise(n())
```


```{r}
tacc3_combined %>% filter(has_cancer == "Cancer", above_95 == TRUE) %>% distinct(rail_id)
tacc3_combined %>%
  ungroup() %>%
  filter(has_cancer == "Cancer") %>%
  filter(Project_ID == "BLCA" | Project_ID == "BRCA" | Project_ID == "CESC" | Project_ID == "ESCA" | Project_ID == "GBM" | Project_ID == "HNSC" | Project_ID == "KIRP" | Project_ID == "LAML" | Project_ID == "LGG" | Project_ID == "LIHC" | Project_ID == "LUAD" | Project_ID == "LUSC" | Project_ID == "STAD") %>%
  filter(above_95 == TRUE)
```