In guokai8/bioAnno: Build Annotation From Online Database

bioAnno An R package for building annotation package by using information from KEGG, NCBI, Ensembl and return OrgDb object such as org.Hs.eg.db.

1. Introduction

With the increasing of high throughput data generated, the requirement for having annotation package is necessary for people who want to do functional enrichment analysis, id conversion and other type related analysis. bioAnno provides wrap functions include fromKEGG, fromEnsembl, fromNCBI and fromAnnoHub to build annotation package. Making Organism Packages is a straightforward process using the helper functions fromKEGG, fromNCBI and from fromAnnoHub. Moreover, users are also allowed to make their own package based on their own annotation file by using fromOwn.

2. Software Usage

2.1 Installation

The package can be installed with following command ``` {r install, eval = FALSE} if (!requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install("bioAnno")

### 2.2 Load package 
```r
library(bioAnno)

2.3 How to use it

``` {r quick, message=FALSE} library(bioAnno)

build E.coli annotation package by using fromKEGG function from

KEGG database.

fromKEGG(species="eco", install = FALSE)

which will build "org.eco.eg.db" package. The package contains

KEGG, GO annotation. You can use install = TRUE to direct

install the package.

build from arabidopsis thaliana annotation package by using fromAnnHub

function

fromAnnHub(species="ath", install = FALSE)

### 2.4 Main Functions
--  _fromKEGG_ build annotation package by extracting annotation information 
    from Kyoto Encyclopedia of Genes and Genomes (KEGG) database. 
    You can use KEGG species code as the query name.

-- _fromNCBI_ build annotation package by extracting annotation information from
    NCBI database.

-- _fromENSEMBL_ build annotation package by extracting annotation information 
    fromENSEMBL database. It includes function to build annotaion package for 
    plant with parameter plant = TRUE.  

-- _fromAnnhub_ build annotation package with the AnnotationHub package 

-- _getTable_ get annotataion table from temporary package which need user provide the temporary path

## 3 To use the annotation package user created
An organism level package (an ‘org’ package) you created uses a central gene 
identifier and contains mappings between this identifier and other kinds of
identifiers. The most common interface for retrieving data is the _select_
method.
```r
#First make your own anntation package and loading the package
data(ath)
fromOwn(geneinfo = ath, install = TRUE)
library(org.species.eg.db)

There are 4 common methods that work together to allow a select interface. The 1st one is columns, which help you to discover which sorts of annotations can be extracted from it.

columns(org.species.eg.db)

The next method is keytypes which tells you the kinds of things that can be used as keys.

keytypes(org.species.eg.db)

The third method is keys which is used to retrieve all the viable keys of a particular type.

key <- keys(org.species.eg.db,keytype="ENTREZID")

And finally there is select, which extracts data by using values supplied by the other method

result <- select(org.species.eg.db, keys=key,
columns=c("GID","GO","PATH"),keytype="ENTREZID")
head(result)

Users are also allowed to use mapIds extract gene identifiers KEGG pathway from the annotation package.

KEGG<-mapIds(org.species.eg.db,keys=key,column="PATH",keytype="ENTREZID")
head(KEGG)

Or for id conversion

mapIds(org.species.eg.db,keys=key[1:10],column="GID",keytype="ENTREZID")

The version number of R and packages loaded for generating the vignette were:

sessionInfo()

guokai8/bioAnno documentation built on May 8, 2023, 12:42 p.m.