annots_from_fa_df: Get genome annotation from Ensembl FASTA file

In BUSpaRse: kallisto | bustools R utilities

Description

Ensembl FASTA files for RNA contain much of the information contained in GTF files, such as chromosome, genome assembly version, coordinates, strand, gene ID, gene symbol, and gene description. Given such a FASTA file, this function can extract all the genome annotation information and return a data frame or a GRanges object.

Usage

annots_from_fa_df(file)

annots_from_fa_GRanges(file)

Arguments

file	Path to the FASTA file to be read. The file can remain gzipped.

Value

annots_from_fa_df returns a data frame and annots_from_fa_GRanges returns GRanges.

A data frame with genome annotations.

Examples

fn <- system.file("testdata/fasta_test.fasta", package = "BUSpaRse")
annots_from_fa_df(fn)
annots_from_fa_GRanges(fn)

BUSpaRse documentation built on March 3, 2021, 2:01 a.m.