designPrimers: Design primers for amplicons

Description Usage Arguments Author(s) See Also

Description

Designs primers for Amplicon Bisulfite sequencing experiments

Usage

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designPrimers(target, genome, tag = NULL, primer3 = NULL, settings = NULL,
  thermoParam = NULL, sizeRange = c(151, 500), Tm = c(55, 57, 58),
  ncores = 4)

Arguments

target

DNAStringSet or GRanges object. If it is a GRanges object you need to provide BSgenome package with it. If it is a DNAStringSet object then names argument should contain chromomsome,start and end, by following "chr_start_end" naming convetion.

genome

default is NULL, it needs to be set only if target is set to be a GRanges object

tag

extra information about amplicons, this will be concatanated to the names of BioStringSet object which is either created internally or provided by the user by supplying 'target' argument with a BioStringSet object

primer3

the filesystem path to primer3 executable, default value NULL will use the version installed with the package

settings

text file for p3 settings. Default value NULL will use the default settings file installed with the package.

termoParam

Location for thermodynamic parameters for primer3, this should designate a directory, not a single file. Default value NULL, will use the directory that is installed with the package.

sizeRange

a two element vector of integers for size range of the amplicons

Tm

a three element vector having minimum,optimum and maximum melting tempratures for primer desing (in that order).

ncores

number of cores to run on. default=1

Author(s)

Based on Arnaud Krebs' function, modified by Altuna Akalin

See Also

primers2ranges, filterPrimers


BIMSBbioinfo/AmpliconBiSeq documentation built on May 5, 2019, 10:25 a.m.