(2/N) Pre-release data QC

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

quality control of v13 data

What was your approach?

Methylation-related data is downloaded following the code change in this PR (#415).
Delete snv_dgd related code and run analyses/data-pre-release-qc module

What GitHub issue does your pull request address?

#395

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

Which areas should receive a particularly close look?

analyses/data-pre-release-qc/results
01-data-harmonization-qc.Rmd

Is there anything that you want to discuss further?

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

Yes

Results

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

Table

What is your summary of the results?

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 we have some samples which are not in histologies and need to be removed from these merge matrices. In the meantime, could you stack this PR on #413 and update the one bit for sourcing data from /data

[jharenza]

@zzgeng for line 9, can you use Sys.Date() here so that the date of the run prints out in the HTML file. Also can you go through and fix the few "histologies" typos ("histolgies") and revert back to using the data folder?

[jharenza]

@zzgeng maybe we should close this and open a new one stacked on the v13 release pr so it's cleaner