SigMA2 documentation: example files
===================================

The files the SigMA2 pages at https://sigscape.org/docs/sigma2 download, so every
Input block on a page runs on a fresh install of the package. Each page names the
file it needs in a bash block; nothing on a page assumes a file that is not here
or at a public URL the page shows.

msk_breast_50_segments.seg
  Copy-number segments for the fifty MSK-IMPACT 2017 breast panels of SigMA (R)'s
  example MAF (test_mutations_50sample.maf, from the SigMA repository). Log-ratio
  segments in the cBioPortal .seg format (ID, chrom, loc.start, loc.end, num.mark,
  seg.mean), hg19. Source: the MSK-IMPACT 2017 cohort on cBioPortal. Used by the
  "Fifty breast panels" example to run the HRD model's tcn variant.

tcga_brca_ascat_segments.tsv
  Allele-specific copy-number segments (ASCAT: sample, chr, startpos, endpos,
  nMajor, nMinor), hg19, for six TCGA breast tumors that are also in SigMA (R)'s
  TCGA breast MAF (tcga_mc3_brca.maf). Used by the "HRD on exomes" example to run
  the HRD model's gis variant.

exposures_template.csv
  The header of the exposure table the training example expects: one row per
  genome and one column per signature of the cosmic_v3p2_inhouse catalog. The
  rows are yours; this file shows the columns and their order.

The mutation files themselves are SigMA (R)'s public example data and are
downloaded from the SigMA repository by the pages that use them, under SigMA's
license.
