qSig-class: Class "qSig"

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Class "qSig"

Description

S4 object named qSig containing query signature information for Gene Expression Signature (GES) searches. It contains slots for query signature, GESS method and path to the GES reference database.

Slots

query

If 'gess_method' is one of 'CMAP' or 'LINCS', this should be a list with two character vectors named upset and downset for up- and down-regulated gene labels (here Entrez IDs), respectively.

If 'gess_method' is 'gCMAP', 'Fisher' or 'Cor', a single column matrix with gene expression values should be assigned. The corresponding gene labels are stored in the row name slot of the matrix. The expected type of gene expression values is explained in the help files of the corresponding GESS methods.

gess_method

one of 'CMAP', 'LINCS', 'gCMAP', 'Fisher' or 'Cor'

refdb

character(1), can be "cmap", "cmap_expr", "lincs", "lincs_expr", or "lincs2" when using existing CMAP/LINCS databases.

If users want to use a custom database, it should be the file path to the HDF5 file generated with the build_custom_db function. Alternatively, source files of the CMAP/LINCS databases can be used as explained in the vignette of the signatureSearchData package.

db_path

character(1), file path to the refdb

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.