rGO2TR: rGO2TR: filters NCBI Annotated Eukaryotic Genomes by gene...

In jelber2/rGO2TR: Filters NCBI Annotated Eukaryotic Genomes by Gene Ontology.

rGO2TR: filters NCBI Annotated Eukaryotic Genomes by gene onotology.

Description

The rGO2TR package is based off of the GO2TR: Gene Ontology to Target Region workflow and includes functions for manipulating gene annotations, acquiring mRNA accession identifiers, creating a gene ontology list, and filtering gene annotations by gene ontology.

rGO2TR functions

Note: All functions are listed in chronological order.

Also see the [README](https://github.com/jelber2/rGO2TR/blob/master/README.md) for full program details.

The gene annotation functions include: get.ncbi.annot.euk.genomes - gets all available genomes annotated by NCBI Eukaryotic Genome Annotation Pipeline, search.annot.euks - searches for a specified species, and get.gff3 - downloads the gene annotations for the specified species.

The mRNA accession functions include: filter.gff3 - filters gene annotations by desired source (i.e., CDS, mRNA, exon, etc.), get.mRNA.acc - searches through filtered gene annotations for predicted mRNA accessions identifiers (i.e., "XM_"), get.mRNA.translated - returns the protein translated sequences for the mRNA in FASTA format, upload.fasta.to.goanna - uploads protein FASTA files to GOanna, and download.goanna.results - saves the output of goanna as a dataframe.

The gene ontology list functions are not coded as package functions, rather they are simple commands such as the following example, which creates a GO identitifer list (inlcudes descendant/offspring terms) for the GO term pigment:

GO.term <- "GO:0043473" # sets pigment as base GO term

GO.term.descendants <- GOBPOFFSPRING$"GO:0043473" # the offspring/descendant GO terms for pigment

GO.id.list <- c(GO.term, GO.term.descendants) # combines base and descendant terms

The filtering gene annotation by gene onotlogy functions include: make.mRNA.GO.list - processes output from the GOanna program, which is used to assign gene ontology terms to mRNA, filter.mRNA.GO.list - filters themRNA.GO.list by GO.id.list to create a retained mRNA list to eventually filter the gene annotations, create.target.region - filters the gene annotations by the retained mRNA, effectively creating a pigmentome for example, and save.target.region.as.bed.file exports the generated target region into the bed (Browser Extensible Data) format.

jelber2/rGO2TR documentation built on Feb. 22, 2024, 12:50 p.m.