config.yml

default:
  counts:
    synID: syn22084837
    version:
    gene id: feature
  metadata:
    synID: syn22090070
    version: 2
    sample id: sampleID
  biomart:
    synID: syn21907998
    version:
    filters: ensembl_gene_id
    host: ensembl.org
    organism: hsa
    exon only: FALSE
    custom build: FALSE
    gtfID:
    gtfVersion:
    fastaID:
    fastaVersion:
  factors: ["sampleID", "batch", "sex", "diagnosis"]
  random_effect:
  continuous: ["RIN", "pmi", "ageofdeath"]
  x_var: diagnosis
  cores: 6
  conditions: ["diagnosis", "sex"]
  cpm threshold: 1
  percent threshold: 0.5
  sex check: sex
  dimensions:
    color: "diagnosis"
    shape: "batch"
    size: "ageofdeath"
  skip model: TRUE
  force null model: 
  force model with: ["sex", "diagnosis", "batch"]
  de FC: 1.5
  de p-value threshold: 0.05
  visualization gene list: ["LCN2", "TRIM69"]
  de contrasts:
    diagnosis:
      primary: ["diagnosis"]
      is_numeric_int: FALSE
      numeric:
      contrasts: ["CT-ZZ"]
    diagnosis-sex:
      primary: ["diagnosis", "sex"]
      is_numeric_int: FALSE
      numeric:
      contrasts: ["ZZ_F-CT_F","ZZ_M-CT_M" ]
    age-death:
      primary: ["diagnosis"]
      is_numeric_int: TRUE
      numeric: ["ageofdeath"]
      contrasts: ["CT-ZZ"]
  report: "openSci"
  store output: syn23572479