sequence_attributes: Gather some simple sequence attributes.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Gather some simple sequence attributes.

Description

This extends the logic of the pattern searching in pattern_count_genome() to search on some other attributes.

Usage

sequence_attributes(fasta, gff = NULL, type = "gene", key = NULL)

Arguments

fasta	Genome encoded as a fasta file.
gff	Optional gff of annotations (if not provided it will just ask the whole genome).
type	Column of the gff file to use.
key	What type of entry of the gff file to key from?

Value

List of data frames containing gc/at/gt/ac contents.

See Also

[Biostrings] [Rsamtools]

Examples

 pa_data <- get_paeruginosa_data()
 pa_fasta <- pa_data[["fasta"]]
 pa_gff <- pa_data[["gff"]]
 pa_attribs <- sequence_attributes(pa_fasta, gff = pa_gff)
 head(pa_attribs)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.