moa_conn: Summarize GESS Results on MOA Level

In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Description

Function summarizes GESS results on Mode of Action (MOA) level. It returns a tabular representation of MOA categories ranked by their average signature search similarity to a query signature.

Usage

moa_conn(gess_tb, moa_cats = "default", cells = "normal")

Arguments

gess_tb	tibble in gessResult object
moa_cats	if set as "default", it uses MOA annotations from the CLUE website (https://clue.io). Users can customize it by providing a 'list' of character vectors containing drug names and MOA categories as list component names.
cells	one of "normal", "cancer" or "all", or a character vector containing cell types of interest. "all": all cell types in LINCS database; "normal": normal cell types in LINCS database as one group; "tumor": tumor cell types in LINCS database as one group;

Details

Column description of the result table:

moa: Mechanism of Action (MOA)

cells: cell type information

mean_rank: mean rank of drugs in corresponding GESS result for each MOA category

n_drug: number of drugs in each MOA category

Value

data.frame

See Also

gessResult

Examples

res_moa <- moa_conn(dplyr::tibble(
                    pert=c("vorinostat", "trichostatin-a", "HC-toxin"), 
                    cell=rep("SKB",3), 
                    pval=c(0.001,0.02,0.05)))

signatureSearch documentation built on April 16, 2021, 6 p.m.