extract: Extract amplicons from sequences from 'insilicoPCR' object

Description Usage Arguments Value Examples

View source: R/insilico.R

Description

Extract amplicons from sequences from insilicoPCR object

Usage

1

Arguments

x

object of class insilicoPCR

Value

object of class DNAStringSet

Examples

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##Run local primer blast

query <- readDNAStringSet("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/010/525/GCA_000010525.1_ASM1052v1/GCA_000010525.1_ASM1052v1_genomic.fna.gz")

primers <- c("GGCTGGATCACCTCCTT","GCCWAGGCATCCDCC")
db <- makeprimerdb(primers)

#Define BLAST arguments: these are the same that can be found in `RinsilicoPCR::blast.params$primers`
args <- list(
		outfmt="'6 qacc sacc pident length qlen slen qstart sstart qend send evalue'",
		max_target_seqs=20,
		word_size=8
		)

blastres <- blast(query,db,args)

pairs <- primer.insilico(blastres)

amplicons <- extract(pairs)

zachth/RinsilicoPCR documentation built on Nov. 18, 2017, 11:27 p.m.