<Drug> GESS/FEA analysis

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

suppressPackageStartupMessages({
    library(signatureSearch); 
    library(readr); library(dplyr); library(DT)
})

Short Introduction

This vignette shows the code and results for Gene Expression Signature Searches (GESS) with the downstream Functional Enrichment Analysis (FEA) of the query in cell. The introduction of GESS and FEA as well as their corresponding methods is available at this vignette of the signatureSearch package. Here, <gess_method> is used as GESS method, The <N_gess_drugs> top ranking unique hits in the GESS table were then used for FEA where three different annotation systems were used: GO Molecular Function (GO MF), GO Biological Process (GO BP) and KEGG pathways.

GESS/FEA workflow

wf_list <- runWF(drug="<drug>", cell="<cell>", refdb="<refdb>", 
                 gess_method="<gess_method>", fea_method="<fea_method>", 
                 N_gess_drugs=<N_gess_drugs>)

GESS/FEA results

GESS

options(DT.options = list(lengthMenu=c(10, 20, 50), scrollX=TRUE, autoWidth=TRUE))
gess_tb <- suppressMessages(read_tsv("results/<gess_method>_res.tsv"))
tar_short <- tarReduce(gess_tb$'t_gn_sym')
gess_tb$'t_gn_sym' <- tar_short
datatable(gess_tb[1:100, ], filter = 'top', escape=FALSE) %>%
        formatSignif(columns=sapply(gess_tb, class)=="numeric", digits=3)

Full table

GO MF

mf_tb <- suppressMessages(read_tsv("results/<fea_method>_mf_res.tsv"))
datatable(mf_tb[1:50, colnames(mf_tb) != "itemID"], filter = 'top', escape=FALSE) %>%
        formatSignif(columns=sapply(mf_tb, class)=="numeric", digits=3)

Full table

GO BP

bp_tb <- suppressMessages(read_tsv("results/<fea_method>_bp_res.tsv"))
datatable(bp_tb[1:50, colnames(bp_tb) != "itemID"], filter = 'top', escape=FALSE) %>%
        formatSignif(columns=sapply(bp_tb, class)=="numeric", digits=3)

Full table

KEGG

kegg_tb <- suppressMessages(read_tsv("results/<fea_method>_kegg_res.tsv"))
datatable(kegg_tb[1:50, colnames(kegg_tb) != "itemID"], filter = 'top', escape=FALSE) %>%
        formatSignif(columns=sapply(kegg_tb, class)=="numeric", digits=3)

Full table

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