addGESSannot: Add Compound Annotation Info to GESS Result Table

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

Add Compound Annotation Info to GESS Result Table

Description

This function supports adding customized compound annotation table to the GESS result table if provided. It then automatically adds the target gene symbols, MOAs and PubChem CID columns (t_gn_sym, MOAss, PCIDss) if the table contains a column that stores compound names.

Usage

addGESSannot(
  gess_tb,
  refdb,
  cmp_annot_tb = NULL,
  by = "pert",
  cmp_name_col = "pert"
)

Arguments

gess_tb	tibble or data.frame object of GESS result, can be accessed by the result method on the gessResult object from gess_* functions. Or a customized data frame that contains a pert column that stores compound id or name.
refdb	character(1), reference database that can be accessed by the refdb method on the gessResult object. If gess_tb is a customized table, refdb can be just set as 'custom'.
cmp_annot_tb	data.frame or tibble of compound annotation table. This table contains annotation information for compounds stored under pert column of gess_tb. Set to NULL if not available. This table should not contain columns with names of "t_gn_sym", "MOAss" or "PCIDss", these three columns will be added internally and thus conserved by the function. If they are contained in cmp_annot_tb, they will be overwritten. If users want to maintain these three columns in the provided annotation table, give them different names.
by	character(1), column name in cmp_annot_tb that can be merged with pert column in gess_tb. If refdb is set as 'lincs2', it will be merged with pert_id column in the GESS result table. If cmp_annot_tb is NULL, by is ignored.
cmp_name_col	character(1), column name in gess_tb or cmp_annot_tb that store compound names. If there is no compound name column, set to NULL. If cmp_name_col is available, three additional columns (t_gn_sym, MOAss, PCIDss) are automatically added by using get_targets, CLUE touchstone compound MOA annotation, and 2017 lincs_pert_info annotation table, respectively as annotation sources. t_gn_sym: target gene symbol, MOAss: MOA annotated from signatureSearch, PCIDss: PubChem CID annotated from signatureSearch.

Value

tibble of gess_tb with target, MOA, PubChem CID annotations and also merged with user provided compound annotation table.

Examples

gess_tb <- data.frame(pert=c("vorinostat", "sirolimus", "estradiol"),
                  cell=c("SKB", "SKB", "MCF7"),
                  NCS=runif(3))
cmp_annot_tb <- data.frame(pert_name=c("vorinostat", "sirolimus", "estradiol"),
                           prop1=c("a", "b", "c"),
                           prop2=1:3)
addGESSannot(gess_tb, "custom", cmp_annot_tb, by="pert_name", 
             cmp_name_col="pert")

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