all_columns: []
columns:
  positionCol: Position
  quantCols:
  - alias: CTRL
    column: QUANT_CTRL
    group_name: Group_1
    group_rank: 0
    sample_index: 1
  - alias: CTRL_1
    column: QUANT_CTRL_1
    group_name: Group_1
    group_rank: 0
    sample_index: 2
  - alias: CTRL_2
    column: QUANT_CTRL_2
    group_name: Group_1
    group_rank: 0
    sample_index: 3
  - alias: THZ1
    column: QUANT_THZ1
    group_name: Group_2
    group_rank: 1
    sample_index: 4
  - alias: THZ1_1
    column: QUANT_THZ1_1
    group_name: Group_2
    group_rank: 1
    sample_index: 5
  - alias: THZ1_2
    column: QUANT_THZ1_2
    group_name: Group_2
    group_rank: 1
    sample_index: 6
  - alias: U0126
    column: QUANT_U0126
    group_name: Group_3
    group_rank: 2
    sample_index: 7
  - alias: U0126_1
    column: QUANT_U0126_1
    group_name: Group_3
    group_rank: 2
    sample_index: 8
  - alias: U0126_2
    column: QUANT_U0126_2
    group_name: Group_3
    group_rank: 2
    sample_index: 9
  residueCol: Residue
  upidCol: ID
databases:
  phosphositeplus: true
  signor: true
  sukiyama_et_al: false
is_example: false
n_groups:
  n_groups: 3
processing:
  filtering:
    doFiltering: false
    filterTerms:
    - "CON_\r"
    - REV_
    minValues: 0
    minValuesIn: group
  imputation:
    doImputation: false
    imputeCategory: group
    imputeType: minimum
  normalisation:
    doNormalisation: false
    normalisationType: none
  transformation:
    already_logged: false
    doTransformation: true
    log_base: 2
    transformationType: log2