gessResult-class {signatureSearch} | R Documentation

## gessResult object

### Description

The `gessResult` object organizes Gene Expression Signature Search (GESS) results. This includes the main tabular result of a GESS, its query signature, the name of the chosen GESS method and the path to the reference database.

### Slots

`result`

  tibble object containing the search results for each perturbagen (e.g. drugs) in the reference database ranked by their signature similarity to the query. The result table can be extracted via the `result` accessor function.

  Descriptions of the columns common among the tabular results of the individual GESS methods are given below. Note, the columns specific to each GESS method are described in their help files.

  - pert: character, name of perturbagen (e.g. drug) in the reference database

  - cell: character, acronym of cell type

  - type: character, perturbation type. In the CMAP/LINCS databases provided by `signatureSearchData`, the perturbation types are currently treatments with drug-like compounds (trt_cp). If required, users can build custom signature database with other types of perturbagens (e.g., gene knockdown or over-expression events) with the provided `build_custom_db` function.

  - trend: character, up or down when the reference signature is positively or negatively connected with the query signature, respectively.

  - N_upset: integer, number of genes in the query up set

  - N_downset: integer, number of genes in the query down set

  - t_gn_sym: character, symbol of the gene encoding the corresponding drug target protein

`query`

  query signature

`gess_method`

  name of the GESS method

`refdb`

  path to the reference database

[Package signatureSearch version 1.0.4 Index]