gessResult-class: gessResult object

In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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

signatureSearch documentation built on April 16, 2021, 6 p.m.