Commit c777358f authored by Thomas Schwarzl's avatar Thomas Schwarzl
Browse files

add table

parent fa71a401
......@@ -296,12 +296,12 @@ depricated, just 2C short
```{r}
onlyTRIC2 <- RA$add_annotation(name = "only_2C_TRIC2",
values =
RA$get_main_table() %>%
mutate(property = ! (!!sym(SRIC_2)) &
!!sym(TRIC_2)
) %>%
pull(property) )
values =
RA$get_main_table() %>%
mutate(property = ! (!!sym(SRIC_2)) &
!!sym(TRIC_2)
) %>%
pull(property) )
```
......@@ -363,6 +363,18 @@ TRAPP_id <- RA$add_annotation(name = "TRAPP",
```
### Protein Coding
```{r}
protein_coding <- RA$add_annotation(name = "protein_coding",
values =
RA$get_main_table() %>%
mutate(property = RBPANNO000000069.1 == "protein_coding"
) %>%
pull(property) )
```
### Found in more than 20 studies
......@@ -629,12 +641,20 @@ RA$save_euler(selection_ids = c(TRIC, TRIC_2, SRIC_2),
### TRIC / TRAPP / any Sc
```{r}
RA$save_venn(selection_ids = c(TRIC, anyScExpTRAPP_id, TRAPP_id),
names = c("TRIC", "any Sc RIC", "any TRAPP"),
file_root = file.path(output_dir, "TRIC_anySc_TRAPP"),
fill = cbbPalette[c(6,7,3)])
RA$save_venn(selection_ids = c(TRIC, anyScExpTRAPP_id, TRAPP_id),
names = c("TRIC", "any Sc RIC", "any TRAPP"),
file_root = file.path(output_dir, "TRIC_anySc_TRAPP_venn"),
fill = cbbPalette[c(6,7,3)])
```
```{r}
RA$save_euler(selection_ids = c(TRIC, anyScExpTRAPP_id, TRAPP_id),
names = c("TRIC", "any Sc RIC", "any TRAPP"),
file_root = file.path(output_dir, "TRIC_anySc_TRAPP_euler"),
fill = cbbPalette[c(6,7,3)])
```
### Short
```{r}
......@@ -832,9 +852,20 @@ EHE <- EnrichmentHandler$new()
EHE$add_comparison_manually("SRIC",
get_ids(RA$get_main_table(), SRIC_2),
get_ids(RA$get_main_table(), background_run2))
EHE$add_comparison_manually("TRIC2",
get_ids(RA$get_main_table(), TRIC_2),
background_run1_run2)
EHE$add_comparison_manually("TRIC2pc",
get_ids(RA$get_main_table(), TRIC_2),
get_ids(RA$get_main_table(), protein_coding))
EHE$add_comparison_manually("TRICpc",
get_ids(RA$get_main_table(), TRIC),
get_ids(RA$get_main_table(), protein_coding))
EHE$add_comparison_manually("TRIC",
get_ids(RA$get_main_table(), TRIC),
background_run1_run2)
......@@ -876,6 +907,24 @@ EHN$add_comparison_manually("TRIC2",
type = "Entrez"),
background_run1_run2_entrez)
EHN$add_comparison_manually("TRIC2pc",
get_ids(RA$get_main_table(),
TRIC_2,
type = "Entrez"),
get_ids(RA$get_main_table(),
protein_coding,
type = "Entrez"))
EHN$add_comparison_manually("TRICpc",
get_ids(RA$get_main_table(),
TRIC,
type = "Entrez"),
get_ids(RA$get_main_table(),
protein_coding,
type = "Entrez"))
EHN$add_comparison_manually("TRIC",
get_ids(RA$get_main_table(),
TRIC,
......@@ -1080,6 +1129,14 @@ gly %>% separate_rows(EntrezIDs, sep = ",") %>%
"cyto_glycolysis.tsv"))
```
## Save Table
```{r}
write.xlsx(RA$get_main_table(descriptive_names = T),
file = file.path(output_dir, "fulltable.xlsx"))
```
# Session
```{r}
......
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