comPyDEtools/compydetools/data/synthetic_conditions.yaml at main · 136s/comPyDEtools · GitHub

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%YAML 1.2
---
# analysis command and result
analysis: !!map
  cmds: !!seq
    - !!str some commands to analysis by line
  # {count_stem} replaced by dataset stem
  # {method_type} replaced by method_type
  res: !!str regex/of/path/to/result/files
  # colname of true deg regulation (up, dn or ns)
  de_true: !!str Description
  # colname of deg score (like p-value)
  de_score: !!str padj
  de_score_threshold: !!float 0.1

# directory
dirs: !!map
  dataset: input
  result: result

# KIRC, Bottomly, mKdB, mBdK
simul_data: !!seq
  - KIRC

# same, different
disp_type: !!seq
  - same

# float 0-1
frac_up: !!seq
  - 0.5

# int 3-
nsample: !!seq
  - 3
  - 10

# D, R, OS, DL
outlier_mode: !!seq
  - D
  - R
  - OS

# float 0-100
pde: !!seq
  - 5
  - 10
  - 30
  - 60

# auc, tpr, fdr, f1score, kappa, cutoff
metrics_type: !!seq
  - auc
  - tpr
  - fdr

# specify your dict("method name in path of DE results": "method name in figures",)
method_type: !!map
  deseq2: Deseq2

# int 3-
nrep: !!int 50