/org.Osativa.eg.db

Primary LanguageR

DOI

org.Osativa.eg.db

Introduction

The Orazy sativa simple organism annotation for GO enrichment analysis, and ID conversion between MSU and RAP

水稻的物种注释包, 方便用在clusterProfiler里进行GO富集分析, 以及MSU和RAP-DB之间的ID转换

Installation

Required:

  • R > 3.5.1
  • AnnotationDbi > 1.44.0
install.packages("https://github.com/xuzhougeng/org.Osativa.eg.db/releases/download/v0.01/org.Osativa.eg.db.tar.gz", 
    repos = NULL, 
    type="source")

Usage

Load the packages

library(org.Osativa.eg.db)
org <-org.Osativa.eg.db

Convert RAP-DB ID to MSU LOC-ID: Os03g0831400 -> LOC_Os03g61590

# rap_id: RPA-DB ID
map_id <- AnnotationDbi::select(org, keys = rap_id, 
                                columns=c("GID"), keytype = "RAP")

Convert MSU LOC-ID to RAP-DB ID: LOC_Os03g61590 -> Os03g0831400

# msu_id: MSU ID
map_id <- AnnotationDbi::select(org, keys = rap_id, 
                                columns=c("RAP"), keytype = "GID")

GO enrichment anlysis using clusterProfiler enrichGO

ego <- enrichGO(rap_id,
        OrgDb = org,
        keyType = "RAP",
        ont="BP")

For more information about clusterProfiler, please go to https://guangchuangyu.github.io/software/clusterProfiler/documentation/

Citation

If you use the org.Osativa.eg.db in your project, it is very nice for you to cite it

xuzhougeng. (2019, August 22). xuzhougeng/org.Osativa.eg.db v0.01 (Version v0.01). Zenodo. http://doi.org/10.5281/zenodo.3374105