Updated analysis: add glialneuronal tumors back to LGAT subtyping

[jharenza]

What analysis module should be updated and why?

molecular-subtyping-LGAT

What changes need to be made? Please provide enough detail for another participant to make the update.

revert the glialneuronal tumor removal #1014 , but reannotate these at the end of the module as per this discussion. We would recode molecular_subtype, == GNT, subtype, instead of LGG, subtype and update the integrated_diagnosis with the appropriate tumor type.

This will enable us to keep the subtyping, which should be the same as LGAT subtyping, for these tumors.

What input data should be used? Which data were used in the version being updated?

same as currently used

When do you expect the revised analysis will be completed?

this week?

Who will complete the updated analysis?

@kgaonkar6

[kgaonkar6]

Just wanted to mention here that molecular-subtyping-pathology will also need an update to recode for glialneuronal tumor
samples. Specifically this code which adds the intgerated_diagnosis for LGG samples:

OpenPBTA-analysis/analyses/molecular-subtyping-pathology/01-compile-subtyping-results.Rmd

Lines 223 to 239 in c074457

	### Handling LGAT
	```{r}
	lgat_results_df <- bind_exp_strategies(lgat_results_df) %>%
	inner_join(select(histologies_df,c(join_cols,
	pathology_diagnosis)),
	by = "Kids_First_Biospecimen_ID") %>%
	mutate(integrated_diagnosis = case_when(
	str_detect(molecular_subtype, "To be classified") ~ NA_character_,
	pathology_diagnosis == "Ganglioglioma" ~ str_replace(molecular_subtype, "LGG, ", "Ganglioglioma, "),
	TRUE ~ str_replace(molecular_subtype, "LGG, ", "Low-grade glioma/astrocytoma, ")
	),
	broad_histology = "Low-grade astrocytic tumor",
	short_histology = if_else(pathology_diagnosis == "Ganglioglioma", "Ganglioglioma", "LGAT"),
	Notes = if_else(!is.na(integrated_diagnosis), "Updated via OpenPBTA subtyping", Notes)
	)

[jharenza]

closed with #1097