getTreats {signatureSearch} | R Documentation |
Get treatment information including perturbation name, cell type and perturbation type from the reference database
getTreats(refdb, sep = TRUE)
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 |
sep |
TRUE or FALSE, whether to separate the treatments or column names of the reference database into 'pert', 'cell' and 'pert_type'. |
character vector if sep
argument is set as FALSE.
Tibble object with 'pert', 'cell', 'pert_type' columns if sep
is TRUE
refdb <- system.file("extdata", "sample_db.h5", package="signatureSearch") treat_info <- getTreats(refdb, sep=TRUE)