{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn5878064, https://www.synapse.org/#!Synapse:syn5842981","dataSubType":"miRNA expression","label":"UQ normalized, filtered","name":"x3t2m1.mature.UQ.mirna.matrix.donor.log","wrangling_procedure":"miRNA matrix data (x3t2m1.mature.UQ.mirna.matrix) are downloaded from synapse, mapped from submitter uuid (all from TCGA) to ICGC specimen id using https://raw.githubusercontent.com/isb-cgc/readthedocs/master/docs/include/LATEST_MANIFEST.tsv, then mapped from specimen id to donor ids using http://pancancer.info/data_releases/may2016/pcawg_sample_sheet.v1.4.2016-09-14.tsv from https://wiki.oicr.on.ca/display/PANCANCER/Available+PCAWG+Data#AvailablePCAWGData-May2016Dataset,Version1.4 . Only tumor data are kept. When multiple tumors are available per donor, the avarage is used as the value for the donor.","type":"genomicMatrix","version":"2017-02-23","unit":"log2(cpm-uq+0.1)","colnormalization":true,"description":"PCAWG-14 miRNA expression (tumors only). UQ normalized miRNA expression matrices. Those contain results for 1864 of 5806 total mature miRNA genes that have passed various filtering steps that are described at https://www.synapse.org/#!Synapse:syn5842981 ."}

{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn8042988, https://www.synapse.org/#!Synapse:syn8042880","dataSubType":"copy number","label":"consensus copy number","name":"20170119_final_consensus_copynumber_sp","assembly":"hg19","type":"genomicSegment","version":"2017-01-19","unit":"total copy number","colnormalization":"normal2","description":"PCAWG-11 consensus segmented copy number. These profiles contain clonal copy number for nearly the complete genomes and are the result of a bespoke procedure that combines output from 6 different copy number callers: ABSOLUTE, ACEseq, Battenberg, CloneHD, JaBbA and Sclust.  PCAWG-11 working group first ran all methods across all samples with the consensus SVs included and applied an algorithm across the segmentations to obtain consensus breakpoints. With these mandatory breakpoints the methods were rerun without calling any additional breakpoints.<br><br>Samples for which the methods disagreed on the ploidy have gone through an adjustment algorithm that applies various ploidy adjustments in order to maximise the agreement and were assessed through a rigorous review procedure. After obtaining consensus on the ploidy segments are considered individually to assign copy number states: Clonal agreement (3 stars), majority vote agreement and agreement after rounding subclonal copy number (2 stars) and a call from the best method on that sample (1 star). This finally yields a complete, clonal copy number profile.<br><br>"}