Add information about thresholded tumor purity analysis to the manuscript

[jaclyn-taroni]

We'll include the panels where we removed tumors below a certain tumor purity threshold in a supplemental figure (related: AlexsLemonade/OpenPBTA-analysis#1691).

We need to address the following:

1. Add a comment to the manuscript that reflects that the results after removing tumors below a certain tumor purity threshold are broadly consistent with the results presented in the main text. There are at least two places we could think about adding this: i. in the section on transcriptomics results ii. in the limitations of the study (i.e., some low purity samples are included in the dataset)
2. We need to add the thresholded tumor purity analysis to the methods section. This should include our rationale. For example, we were concerned about using ESTIMATE because it's not clear that it would be an appropriate method given the tumor types in the dataset. We elected, then, to use tumor purity information derived from WGS data but only when samples where DNA and RNA sequencing were performed on the same extraction (see: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/627ec427ad0a8d9d913e614c9db50546c56d8283/analyses/tumor-purity-exploration/01_explore-tumor-purity.Rmd#L198)
   EDIT We do have some info here: https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/06.methods.md#tumor-purity-tumor-purity-exploration-module but it could be expanded a bit!

This can likely be addressed at the same time as #421.

[jharenza]

ii. in the limitations of the study (i.e., some low purity samples are included in the dataset)

This is taken care of in #435

[jharenza]

Update, all of 1 is included in #433 and all of 2 is updated in #436.

[jharenza]

closed with #433 and #436