Quickly make TxDb object — easyTxDbmaker • plasmoRUtils

A convenience function to make OrgDb packages quickly to be used with other GO enrichment packages such as ClusterProfiler.

Usage

easyTxDbmaker(
  gff,
  fasta,
  abbr = "TgondiiME49",
  org = "Toxoplasma gondii",
  taxid = 508771,
  db = "ToxoDB release 68"
)

Arguments

gff: A link to GFF file from VEuPathDB or path to GFF file if the file is present locally.
fasta: Genome FASTA file obtained from VEuPathDB.
abbr: Abbreviation of the organism.
org: Name of the organism including genus and species.
taxid: NCBI Taxonomy ID. This can be obtained from https://www.ncbi.nlm.nih.gov/taxonomy.
db: Name of the database with release information.

Value

A tar.gz file that can be installed as a package and can be used with GO enrichment tools such as ClusterProfiler.

Examples

if (FALSE) { # \dontrun{
 txdb<-easyTxDbmaker(
 gff="https://toxodb.org/common/downloads/release-68/TgondiiME49/gff/data/ToxoDB-68_TgondiiME49.gff",
 fasta="https://toxodb.org/common/downloads/release-68/TgondiiME49/fasta/data/ToxoDB-68_TgondiiME49_Genome.fasta",
 abbr="TgondiiME49",
 taxid=508771,org = "Toxoplasma gondii ME49",
 db = "ToxoDB release 68")


} # }