README.md

In joshuamwang/CAlbicansR: R wrapper to run CGD Gene Ontology Term Finder

CAlbicansR

This is an R library to analyze biological datasets in Candida albicans. The package relies on publically available data and tools housed at the Candida Genome Database.

Installation

R package installations from Github depend on the install_github() function from devtools.

install.packages('devtools')
library('devtools')
devtools::install_github('joshuamwang/CAlbicansR')
library('CAlbicansR')

Optional: Users are encouraged to run a local instance of Selenium. Specifically, this R library was tested with selenium/standalone-firefox-debug which can be pulled from docker and executed as follows:

# to pull from docker & install
sudo docker pull selenium/standalone-firefox-debug

# to execute
sudo docker run -d -p 4445:4444 -p 5901:5900 --shm-size=4g -e JAVA_OPTS=-Xmx4096m selenium/standalone-firefox-debug

This configuration binds the Selenium port to 4445 and allows for VNC viewer access for debugging on port 5901. More information on debugging Selenium with VNC viewer is available here.

Usage

1. Convert gene names to orf19 values:

genesList <- c("EFG1","WOR1","WOR2")
temp <- nameToOrf(genesList)

print(temp)
EFG1         WOR1         WOR2 
 "orf19.610" "orf19.4884" "orf19.5992"

2. Convert orf19 values to gene names:

orfList <- c("orf19.610","orf19.4884","orf19.5992")
temp <- orfToName(orfList)

print(temp)
orf19.610 orf19.4884 orf19.5992 
    "EFG1"     "WOR1"     "WOR2" 

3. Perform gene ontology enrichment through CGD Gene Ontology Term Finder:

geneList <- c("orf19.610","orf19.4884","orf19.5992","WOR3","AHR1","CZF1")
ontologyType <- "P"   ### P for Process, F for Function, and C for Component
temp <- runGOEnrichment(geneList, ontologyType)

print(temp)

| Gene Ontology term | Corrected P-value | | ------------- |:-------------:| | regulation of phenotypic switching | 3.13e-13 | | positive regulation of phenotypic switching | 1.72e-12 | | phenotypic switching | 1.62e-09 | | regulation of filamentous growth of a population of unicellular organisms | 8.90e-06 | | regulation of filamentous growth | 1.05e-05 | | regulation of single-species biofilm formation | 1.77e-05 | | ... | ... |

joshuamwang/CAlbicansR documentation built on May 17, 2019, 11:17 p.m.