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

In DNAshapeR: High-throughput prediction of DNA shape features

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

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

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)

DNAshapeR documentation built on Nov. 8, 2020, 8:04 p.m.