primer_regions {primers} R Documentation

find the candidate PCR primer design regions from a set of the blastn hits

Description

Usage

primer_regions(blastHits,
    maxCoreSpan = 1000000,
    eval.cutoff = 1,
    primerIds = NULL,
    genome = NULL);

Arguments

blastHits

a collection of the blastn hit records for find the candidate primer design regions, which can be a pipeline object or a vector of the HitRecord object.

maxCoreSpan

the maximum span size in nucleotide of the core primer region. [as integer]

eval.cutoff

the maximum e-value threshold of the accepted blastn hit records. [as double]

primerIds

a character vector of the primer id for filter the input blastn hits. If this parameter is not specified, then all of the input blastn hits will be used for find the candidate regions.

genome

a GFFTable genomics feature annotation table, which is used for annotate the gene context information of the candidate primer regions. If this parameter is not specified, then no gene context information will be calculated. [as GFFTable]

env

the R# runtime environment object. [as Environment]

Details

Authors

seqtoolkit

Value

a vector of the CandidateRegion object, each element in the returned vector is one candidate PCR primer design region with its gene context information;

this function returns a R# error message object if the input blastn hits data can not be cast to a collection of the HitRecord object.

clr value class

Examples

[Package primers version 1.0.0.0 Index]