getTreats: Get Treatment Information

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

Get Treatment Information

Description

Get treatment information including perturbation name, cell type and perturbation type from the reference database

Usage

getTreats(refdb, sep = TRUE)

Arguments

refdb	character(1), one of "lincs", "lincs_expr", "cmap" or "cmap_expr" when using the pre-generated CMAP/LINCS databases or path to the HDF5 file generated with the build_custom_db function. The details is shown in the 'refdb' argument of the qSig function
sep	TRUE or FALSE, whether to separate the treatments or column names of the reference database into 'pert', 'cell' and 'pert_type'.

Value

character vector if sep argument is set as FALSE. Tibble object with 'pert', 'cell', 'pert_type' columns if sep is TRUE

Examples

refdb <- system.file("extdata", "sample_db.h5", package="signatureSearch")
treat_info <- getTreats(refdb, sep=TRUE)

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