Improving PanCancer Atlas Data: (transformation steps for the new data types being added)
The Timeline/Treatment data:
Data Source
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used:
Merge_Clinical.Level_1.20160128(clin.merged.txt) for each cancer type.
Data Transformation
- The detailed transformation steps are listed in the Pull Request here
The Genetic Ancestry data:
Data Source
- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020
- File Used:
Admixture_by_sample.txt(Admix percent by sample) for each cancer type.
The Methylation data:
Data Source
- GDAC Firehose: https://gdc.cancer.gov/node/977
- File Used:
jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv(DNA methylation 450K only beta value data matrix) for each cancer type.
Data Transformation
- The detailed transformation steps are listed in the Pull Request here
- The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina.