Yeast Rank Response Configuration¶

The yeast_rank_response tool requires a json configuration file as input. The configuration file specifies the location of the input files and various other settings.

Below, you will find first an example and next a table defining each key. In the definitions table, if a key/value pair is not marked as [REQUIRED], then there is a default which is set in the tool. [REQUIRED] key/value pairs must be present.

Example¶

{
  "binding_data_path": "path/to/binding/data",
  "binding_source": "eg, 'chipexo_1234' or cc_1234'",
  "binding_identifier_col": "identifier_column_name",
  "binding_effect_col": "effect_column_name_or_none",
  "binding_pvalue_col": "pvalue_column_name_or_none",
  "rank_by_effect": false,
  "expression_data_path": "path/to/expression/data",
  "binding_source": "eg, 'mcisaac_1234' or kemmeren_1234'",
  "expression_identifier_col": "identifier_column_name",
  "expression_effect_col": "effect_column_name_or_none",
  "expression_effect_thres": 0.0,
  "expression_pvalue_col": "pvalue_column_name_or_none",
  "expression_pvalue_thres": 0.05,
  "rank_bin_size": 5,
  "normalize": false,
  "output_file": "rank_response.csv",
  "compress": false
}

Definitions¶

Key	Description
`binding_data_path`	[REQUIRED] Path to the binding data file. The `binding_effect_col`, `binding_pval_col`, and ‘gene_id’ are required.
`binding_source`	[REQUIRED] A description of where the binding data comes from. This might just be the data source, eg ‘chipexo’, or it might be a identifier, eg callingcards_17 or cc_17
`binding_identifier_col`	[REQUIRED] Name of the feature identifier column in the binding data.
`binding_effect_col`	[REQUIRED] Name of the effect column in the binding data. Set to `none` if an effect column does not exist.
`binding_pvalue_col`	[REQUIRED] Name of the pvalue column in the binding data. Set to `none` if a pvalue column does not exist.
`rank_by_effect`	`true` or `false`. Defaults to `false` if not provided. Set to `true` to rank by the binding effect column.
`expression_data_path`	[REQUIRED] Path to the expression data file.
`expression_source`	[REQUIRED] A description of where the expressin data comes from. This might just be the data source, eg ‘mcisaac’, or it might be a identifier, eg mcisaac_17
`expression_identifier_col`	[REQUIRED] Name of the feature identifier column in the expression data.
`expression_effect_col`	[REQUIRED] Name of the effect column in the gene expression data. Set to `none` if an effect column does not exist.
`expression_effect_thres`	[REQUIRED] Threshold for effect expression. Set to `none` if an effect column does not exist
`expression_pvalue_col`	[REQUIRED] Name of the pvalue column in the gene expression data. Set to `none` if a pvalue column does not exist.
`expression_pvalue_thres`	[REQUIRED] Threshold for pvalue of effect expression. Set to `none` if a pvalue column does not exist
`rank_bin_size`	Defaults to 5 if not provided. Bin size for rank response.
`normalize`	This is not currently implemented – it is a placeholder for future development when list input of binding/effect data is supported. `true` or `false`.
`output_file`	Path to the output file. Defaults to `rank_response.csv`.
`compress`	Set this flag to gzip the output file. Defaults to `false`