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SubSCOPE

Job Input Platform Options

Allowed platform types (Required input):

  • MIR, MUTA, GEXP, CNVR, or METH
  • Note: MIR is not available for KIRCKICH and LIHCCHOL

Allowed TCGA Cancer cohort (Optional input):

  • ACC, BLCA, BRCA, CESC, COADREAD, ESCC, GEA, HNSC, KIRCKICH, KIRP, LGGGBM, LIHCCHOL, LUAD, LUSC, MESO, OV, PAAD, PCPG, PRAD, SARC, SKCM, TGCT, THCA, THYM, UCEC, UVM

If no cohort is passed, pan-cancer predictions are made.

User Data Format:

  • First row gives feature IDs.
  • First column gives sample IDs.

Job Outputs

Two files are generated at subscope/data/preds/. The best subtype predictions are included in subscope/data/preds/<platform>-subscope-results.txt.
Note that both outputs will be pre-filtered for only the Cohort of interest, if you specified a TCGA Cancer cohort.

  • <platform>-subscope-results.txt : First column is sample IDs, Second column is the best prediction.

  • <platform>-subscope-confidence.txt : First column is sample IDs, subsequent columns are confidence values for each of the prediction classes.