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org.Calbicans.SC5314.eg.db

This is an org.db annotation resource package for fungal species C. albicans. This annotation package include the gene based information from CGD database.

Install

library(devtools)
devtools::install_github("lakhanp1/fungal_resources/C_albicans/org.Calbicans.SC5314.eg.db")

Usage

To know all the key types for the org.db

library(org.Calbicans.SC5314.eg.db)

AnnotationDbi::keytypes(org.Calbicans.SC5314.eg.db)

C. albicans gene id from CGD database is used as main key column GID in this org.db. To extract all the keys, for example of type GID:

AnnotationDbi::keys(x = org.Calbicans.SC5314.eg.db, keytype = "GID")

## keys using other column
AnnotationDbi::keys(x = org.Calbicans.SC5314.eg.db, keytype = "NCBI_ID")

To extract multiple columns from org.db for gene/s of interest:

## random 1000 genes
gids <- sample(AnnotationDbi::keys(x = org.Calbicans.SC5314.eg.db, keytype = "GID"), 1000)

geneInfo <- AnnotationDbi::select(x = org.Calbicans.SC5314.eg.db,
                                  keys = gids,
                                  columns = c("GID", "GENE_NAME", "KEGG_ID", "DESCRIPTION"),
                                  keytype = "GID")

Applications of org.db package

org.db package has several application while performing genomic data analysis in R. For example:

org.db package can be used to perform GO group assignment analysis using clusterProfiler package.

library(clusterProfiler)

grpGo <- clusterProfiler::groupGO(gene = gids,
                                  OrgDb = org.Calbicans.SC5314.eg.db,
                                  ont = "BP",
                                  level = 4)

Similarly this org.db object can also be used for other functions like enrichGO and gseGO from clusterProfiler package.


To extract gene to GO assignment table for all genes:

geneToGoTab <- AnnotationDbi::select(x = org.Calbicans.SC5314.eg.db,
                                     keys = AnnotationDbi::keys(x = org.Calbicans.SC5314.eg.db, keytype = "GID"),
                                     columns = c("GID", "GOALL"),
                                     keytype = "GID")

head(geneToGoTab)

Please refer to AnnotationDbi package on Bioconductor to learn more on data extraction from org.db.

This package is developed by Chris Lab members at University of Macau, Macau SAR. This is open access package under GNU GPL v2 license.