get_genomic_sequence: Get genomic sequences given ranges
In EricEdwardBryant/mutagenesis: Mutagenesis

Description Usage Arguments Details

Get genomic sequences given ranges

get_genomic_sequence(chr, strand, start, end, genome)

get_genomic_variant(chr, strand, start, end, vcf, genome)

get_coding_sequence(chr, strand, start, end, cds, genome)

get_coding_variant(chr, strand, start, end, cds, vcf, genome)

`chr`	`[character]` Chromosome names. Must match names returned by `names(genome)`.
`strand`	`[character]` Sequence strands (+\|-).
`start`	`[integer]` Start coordinates of ranges.
`end`	`[integer]` End coordinates of ranges
`genome`	`[BSgenome\|DNAStringSet]` A reference genome. See Details.

The reference genome can be either a BSgenome object from a BSgenome reference package (see BSgenome::BSgenome), or a DNAStringSet object (see Biostrings::DNAStringSet). BSgenome objects offer faster sequence aquisition, but are limited to existing BSgenome packages (see BSgenome::available.genomes) whereas DNAStringSet objects can be easily created from any standard FASTA file using Biostrings::readDNAStringSet.

EricEdwardBryant/mutagenesis documentation built on May 14, 2019, 6:13 p.m.