Change the output format in molecular-subtyping-HGG module

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

Change the format of HGG molecular subtype table.

What was your approach?

In the previous version, the molecular subtype table contains three columns for Biospecimen ID, Kids_First_Biospecimen_ID_RNA, Kids_First_Biospecimen_ID_DNA, and Kids_First_Biospecimen_ID_Methyl. In this version, the molecular subtype table only contain one column Kids_First_Biospecimen_ID.

What GitHub issue does your pull request address?

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

07-HGG-molecular-subtyping-combine-table.Rmd
results/HGG_molecular_subtype_tp53.tsv
results/HGG_molecular_subtype.tsv

Is there anything that you want to discuss further?

No

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

Table

What is your summary of the results?

Change the format of HGG molecular subtype table.

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

looks like you are getting an error here:

                           
Quitting from lines 25-39 (10-HGG-TP53-annotation.Rmd) 
Error in `$<-`:
! Assigned data
  `as.character(hgg_subtypes$Kids_First_Biospecimen_ID_RNA)` must be compatible
  with existing data.
✖ Existing data has 1050 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Caused by error in `vectbl_recycle_rhs_rows()`:
! Can't recycle input of size 0 to size 1050.
Backtrace:
 1. base::`$<-`(`*tmp*`, Kids_First_Biospecimen_ID_RNA, value = `<chr>`)
 2. tibble:::`$<-.tbl_df`(...)
 3. tibble:::tbl_subassign(...)
 4. tibble:::vectbl_recycle_rhs_rows(value, fast_nrow(xo), i_arg = NULL, value_arg, call)
  |...................................                 |  67% (unnamed-chunk-2)

[jharenza]

@zzgeng this will need another rerun since #450 was merged

[jharenza]

@zzgeng can you fix merge conflicts here please? Then @rjcorb can you review? Thanks!

[rjcorb]

Looks good to me!