pancan_pcawg_2020 and pan_origimed_2020

[mjsteinbaugh]

Hi Waldron Lab,

I'm working on migrating my cBioPortal workflow code to use cBioPortalData, and the package is really excellent. Great work. One thing that I've noticed is that pancan_pcawg_2020 doesn't appear to be supported by the main cBioPortalData() or cBioDataPack() functions.

I checked using this code:

api <- cBioPortalData:::.loadReportData()[["api_build"]]
pack <- cBioPortalData:::.loadReportData()[["pack_build"]]

See related dataset:
https://www.cbioportal.org/study/summary?id=pancan_pcawg_2020

I'm happy to help add support for this dataset if you guys can walk me through it. One other question I have is what if the package provided download support for pre-processed MultiAssayExperiment objects instead of the pack file approach? Is that doable?

Best,
Mike

[mjsteinbaugh]

Also, the pan_origimed_2020 dataset would be a really helpful addition.

https://www.cbioportal.org/study/summary?id=pan_origimed_2020

[mjsteinbaugh]

Found a minor bug with BiocFileCache call -- usage of cBioDataPack() with ask = FALSE still currently prompts the user to create the cBioPortalData BiocFileCache directory if it doesn't exist.

[LiNk-NY]

Hi Michael, @mjsteinbaugh
I've tested so far with pancan_pcawg_2020 and it looks like only the mutation data can be represented.

cBioDataPack("pancan_pcawg_2020", check_build = FALSE)
Study file in cache: pancan_pcawg_2020
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_cna.txt
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_mirna_zscores.txt
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_mirna.txt
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_mrna_seq_fpkm.txt
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_mutations.txt
Working on: /tmp/RtmpO7UP1B/bb3743edba3_pancan_pcawg_2020/pancan_pcawg_2020/data_timeline_status.txt
harmonizing input:
  removing 18 colData rownames not in sampleMap 'primary'
A MultiAssayExperiment object of 1 listed
 experiment with a user-defined name and respective class.
 Containing an ExperimentList class object of length 1:
 [1] mutations: RaggedExperiment with 382937 rows and 2683 columns
Functionality:
 experiments() - obtain the ExperimentList instance
 colData() - the primary/phenotype DataFrame
 sampleMap() - the sample coordination DataFrame
 `$`, `[`, `[[` - extract colData columns, subset, or experiment
 *Format() - convert into a long or wide DataFrame
 assays() - convert ExperimentList to a SimpleList of matrices
 exportClass() - save data to flat files

You can download the data manually using downloadStudy and take a look at the contents.
I am not sure why the CNA and other datasets are not being built. I will take a closer look later.

Use version 2.9.11 or greater.

Best,
Marcel

[mjsteinbaugh]

Thanks @LiNk-NY I'll take a look and get back to you. I'm primarily interested in the CNA data for both datasets, which I can query via the API but not the main recommended functions in the package.