In Tsmnbx/ZooGVT: A Tool for Analyzing Animal Genomes

library(knitr)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

ZooGVT allows a user to see what Phenotype descriptions have how many genes associated with them from the DgeeDb database

Use the following to download

require("devtools")
devtools::install_github("Tsmnbx/ZooGVT")


library(ZooGVT)

You will also have to download the following from BiocManager

#You will also have to download the following from BiocManager 
require("devtools")
devtools::install_github("Tsmnbx/ZooGVT")
#You will also have to download the following from BiocManager 

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("topGO")

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("biomaRt")

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("BgeeDB")

library(topGO)
library(biomaRt)
library(BgeeDB)
library(ZooGVT)

Components

Here we show the ubronIDS for the phenotype descriptions that we can find for pectoral fin in the zebra Fish

library(ZooGVT)
IdDataFrame<-GetUberonIds("Danio_rerio","Zebrafish","pectoral fin")
IdDataFrame

This is a function that allows puts species wwritten in the correct format for this package:

library(ZooGVT)
NamesSpec<-GetNamesVec("Danio_rerio")

To see what Species we can use for this package that are both in BgeeDB and have phenotype descriptions in ensembl as both are required run ListSpecies()

library(ZooGVT)
ListSpecies()

To see what phenotype descriptions from ensembl are available and what could be used for the feature parameter run ListPhenotypesDescriptions()

library(ZooGVT)
ListPhenotypesDescriptions()

Lets do an example of a species In the code below we ran GenesFromAnatomy to get a radar graph of the number of genes we get for the phenotype descriptions of a feature

AnatomyGeneRadarGraph <-GenesFromAnatomy("Danio_rerio","Zebrafish","pectoral fin")

Here we ran the GeneAnatomyParty to get multiple graphs for the different species for the same feature. Its tricky you have to have an feature that is just precise enough to get good results

library(ZooGVT)
ListofAnimals<-c("Zebrafish","Human")
GeneAnatomyParty(ListofAnimals,"Cardiac")

Package References

Efe, J. (2020) ZooGVT: A R Package For BCB410H. Unpublished.

## Other References

R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

Bastian F et al. (2008). Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. Data Integration Life Sci. Lecture Notes in Computer Science, 5109, 124-31

Martin Morgan (2019). BiocManager: Access the Bioconductor Project Package Repository. R package version 1.30.10. https://CRAN.R-project.org/package=BiocManager

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber, Nature Protocols 4, 1184-1191 (2009).

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma and Wolfgang Huber, Bioinformatics 21, 3439-3440 (2005).

Minato Nakazawa (2019). fmsb: Functions for Medical Statistics Book with some Demographic Data. R package version 0.7.0. https://CRAN.R-project.org/package=fmsb

Tsmnbx/ZooGVT documentation built on Dec. 18, 2021, 5:14 p.m.