qSig-class {signatureSearch} | R Documentation

## 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), repectively.

  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", or "lincs_expr" when using existing CMAP/LINCS databases.

  If users want to use a custom signature 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.

[Package signatureSearch version 1.0.4 Index]