moa_conn {signatureSearch} | R Documentation

## Summarize GESS Results on MOA Level

### 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)))

[Package signatureSearch version 1.0.4 Index]