R: Retrieving annotated sequences

gff2fasta {microseq}

R Documentation

Retrieving annotated sequences

Description

Retrieving from a genome the sequences specified in a gff.table.

Usage

gff2fasta(gff.table, genome)

Arguments

`gff.table`	A `gff.table` (`data.frame`) with genomic features information.
`genome`	A `Fasta` object with the genome sequence(s).

Details

Each row in gff.table (see readGFF) describes a genomic feature in the genome. The information in the columns Seqid, Start, End and Strand are used to retrieve the sequences from genome$Sequence. Every Seqid in the gff.table must match the first token in one of the genome$Header texts.

Value

A Fasta object with one row for each row in gff.table. The Header for each sequence is a summary of the information in the corresponding row of gff.table.

Author(s)

Lars Snipen and Kristian Hovde Liland.

Examples

# Using two files in this package
xpth <- file.path(path.package("microseq"),"extdata")
gff.file <- file.path(xpth,"small.gff")
genome.file <- file.path(xpth,"small_genome.fasta")

# Reading
gff.table <- readGFF(gff.file)
genome <- readFasta(genome.file)

# Retrieving sequences
fasta.obj <- gff2fasta(gff.table,genome)
summary(fasta.obj)
plot(fasta.obj)

[Package microseq version 1.3 Index]