getFasta: Extract fasta sequence given a set of genomic intervals and a...

Description Usage Arguments Value Author(s) Examples

View source: R/getFasta.R

Description

DNAshapeR can predict DNA shape features from custom FASTA files or directly from genomic coordinates in the form of a GRanges object within BioConductor (see <https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html> for more information).

Usage

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getFasta(GR, BSgenome, width = 1e3, filename = 'tmp.fa')

Arguments

GR

A GRanges object indicating genomic coordinates

BSgenome

A BSgenome object indicating the genome of interest

width

A number indicating a fixed width of sequences

filename

The Name of the input fasta format file, including full path to file if it is located outside the current working directory

Value

writes a fasta file

Author(s)

Federico Comoglio

Examples

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gr <- GRanges(seqnames = c("chrI"),
strand = c("+", "-", "+"),
ranges = IRanges(start = c(100, 200, 300), width = 100))
library(BSgenome.Scerevisiae.UCSC.sacCer3)
getFasta(gr, BSgenome = Scerevisiae, width = 100, filename = "tmp.fa")
fn <- "tmp.fa"
pred <- getShape(fn)

TsuPeiChiu/DNAshapeR documentation built on July 6, 2021, 9:07 p.m.