{"name":"consensus.20170217.purity.ploidy_sp","type":"clinicalMatrix","cohort":"PCAWG (specimen centric)","version":"2017-02-22","url":"https://www.synapse.org/#!Synapse:syn8272483, https://www.synapse.org/#!Synapse:syn8042880","label":"tumor purity and ploidy","description":"PCAWG-11 group pooled purity calls across 10 different methods to form a consensus, using both copy number alterations and SNVs. Purities are assigned a confidence by means of the MAD across the available raw purities, where a low value represents high agreement across the purity callers. The ploidy has an additional annotation that denotes the whole genome duplication status of the tumour. A tumour is either duplicated (wgd) or not (no_wgd).<br><br>purity : estimated median purity<br>ploidy : calculated ploidy of the consensus profile<br>purity_conf_mad : confidence in the purity call by means of taking the median absolute deviation across all available raw purity calls<br>wgd_status : whole genome duplication status determined from the consensus copy number profile. A sample is whole genome doubled (wgd) or not (no_wgd)<br>wgd_uncertain : a boolean denoting whether the whole genome duplication is uncertain. Interpret the copy number of these profiles with caution<br><br>","dataSubType":"purity and ploidy"}

{"cohort":"PCAWG (specimen centric)","loader":{"duplicate-keys":{"sampleID":[]},"duplicate-probes":["N:alternative_acceptor:chr6:31237763-31322903","N:alternative_acceptor:chr12:125396727-125397866"]},"url":"https://www.synapse.org/#!Synapse:syn8145655","probeMap":"JuncBASE_alternative_acceptor.probeMap","dataSubType":"alternative splicing events","label":"JuncBASE - alternative acceptor exon-exon junction","name":"JuncBASE_alternative_acceptor.sp.xena","type":"genomicMatrix","version":"2017-03-22","unit":"percent of junction inclusion","description":"Start and end coordinates are the exon-exon junction positions. Alternative acceptor junction inclusion estimated by the JuncBASE method. 100.0 means 100% exon inclusion."}