org.AFumigatus.Af293.eg.db

org.AFumigatus.Af293.eg.db

This is an org.db annotation resource package for fungal species A. fumigatus_Af293. This annotation package include the gene based information from AspGD database.

Install

library(devtools)
devtools::install_github("lakhanp1/fungal_resources/A_fumigatus_Af293/org.AFumigatus.Af293.eg.db")

Usage

To know all the key types for the org.db

library(org.AFumigatus.Af293.eg.db)

AnnotationDbi::keytypes(org.AFumigatus.Af293.eg.db)

A. fumigatus_Af293 gene id from AspGD 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.AFumigatus.Af293.eg.db, keytype = "GID")

## keys using other column
AnnotationDbi::keys(x = org.AFumigatus.Af293.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.AFumigatus.Af293.eg.db, keytype = "GID"), 1000)

geneInfo <- AnnotationDbi::select(x = org.AFumigatus.Af293.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.AFumigatus.Af293.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.AFumigatus.Af293.eg.db,
                                     keys = AnnotationDbi::keys(x = org.AFumigatus.Af293.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.

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