retrieve_longest_isoforms: Retrieve the longest isoforms from a proteome file and save...

In HajkD/orthologr: Comparative Genomics with R

Retrieve the longest isoforms from a proteome file and save results as fasta file

Description

Based on a fasta file storing the peptide isoforms of gene loci and an annotation file in gtf file format, this function extracts the longest isoform per gene locus and stores the results in a new fasta file. This procedure enables easier downstream analyses such as orthology inference etc when dealing with proteome fasta files which usually include isoform peptides.

Usage

retrieve_longest_isoforms(
  proteome_file,
  annotation_file,
  new_file,
  annotation_format = "gff"
)

Arguments

proteome_file	file path to proteome in fasta file format.
annotation_file	file path to the corresponding annotation file in gtf file format.
new_file	file path to new file storing only peptide sequences of the longest isoforms.
annotation_format	format of annotation_file. Options are: annotation_file = "gff" (default) annotation_file = "gtf"

Author(s)

Hajk-Georg Drost

Examples

## Not run: 
# retrieve example data from ENSEMBLGENOMES
proteome <- biomartr::getProteome(db = "refseq", organism = "Arabidopsis thaliana")
annotation <- biomartr::getGFF(db = "refseq", organism = "Arabidopsis thaliana")
# retrieve longest isoforms and store in new file
retrieve_longest_isoforms(proteome_file = proteome, 
                          annotation_file = annotation, 
                          new_file = "Athaliana_pep_longest.fa")
# import new file into R session                          
Athaliana_pep_longest <- Biostrings::readAAStringSet("Athaliana_pep_longest.fa")

## End(Not run)

HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.