review_updates.Rmd

---
title: "Review updates"
output: html_notebook
---

REVIEW UPDATES: Dicussed [here](https://github.com/d3b-center/d3b-pnoc003-HGG-DMG-omics/issues/196#issuecomment-773528346)

### Review updates for CNS_region

release-v19
```{r}
library("tidyverse")
new_hist <- read_tsv("release-v19-20210126/pbta-histologies-base.tsv")
CNS_updates <- read_tsv("input/CNS_region_review_HGG_CK.txt") %>%
  select(sample_id, CNS_Region) %>%
  rename(CNS_region = CNS_Region) %>%
  unique()

new_hist %>%
  left_join(CNS_updates,by="sample_id",suffix=c("_previous","_latest")) %>%
  mutate(CNS_region = case_when(!is.na(CNS_region_latest) ~ CNS_region_latest,
                                TRUE ~ CNS_region_previous)
         ) %>%
  select(-CNS_region_previous,-CNS_region_latest) %>%
  write_tsv("release-v19-20210126/pbta-histologies-base.tsv")
```


hgg-dmg
```{r}
library("tidyverse")
new_hist <- read_tsv("20210126-data/pbta-histologies-base.tsv")
CNS_updates <- read_tsv("input/CNS_region_review_HGG_CK.txt") %>%
  select(sample_id, CNS_Region) %>%
  rename(CNS_region = CNS_Region) %>%
  unique()

new_hist %>%
  left_join(CNS_updates,by="sample_id",suffix=c("_previous","_latest")) %>%
  mutate(CNS_region = case_when(!is.na(CNS_region_latest) ~ CNS_region_latest,
                                TRUE ~ CNS_region_previous)
         ) %>%
  select(-CNS_region_previous,-CNS_region_latest) %>%
  write_tsv("20210126-data/pbta-histologies-base.tsv")
```