Output: Output Functionalities.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Output Functionalities.

Description

write_primers

Writes a set of primers to disk, either as a FASTA or CSV file.

write_settings

Stores primer analysis settings to a file in XML format.

write_templates

Stores a set of templates as a FASTA or CSV file.

create_report

Creates a PDF report for analyzed primer sets.

create_coverage_xls

Creation of an XLS spreadsheet providing an overview of the covered template sequences for each primer. Each cell in the spreadsheet indicates a coverage event between a primer and template using color codes. Identified coverage events are indicated by green, while primer-template pairs without coverage are indicated by red. In case that a primer binding condition (see CoverageConstraints) was active when computing the coverage, the numeric value of the coverage condition is annotated for each cell.

Usage

write_templates(template.df, fname, ftype = c("FASTA", "CSV"))

write_primers(primer.df, fname, ftype = c("FASTA", "CSV"))

create_coverage_xls(primer.df, template.df, fname, settings)

create_report(
  primers,
  templates,
  fname,
  settings,
  sample.name = NULL,
  used.settings = NULL,
  ...
)

write_settings(settings, fname)

Arguments

template.df	An object of class Templates.
fname	The path to the output file.
ftype	A character vector giving the type of the file. This can either be "FASTA" or "CSV" (default: "FASTA").
primer.df	An object of class Primers.
settings	A DesignSettings object to be stored to disk.
primers	To create a report for a single primer set, please provide an evaluated Primers object. For creating a report comparing multiple primer sets, please provide a list of Primers objects.
templates	If primers is a Primers object, templates should be a Templates object. If primers is a list of Primers objects, templates should be a list of Templates objects of the same length as primers.
sample.name	An identifier for your analysis. By default ( NULL), the sample identifier is selected from the Run column of the input templates.
used.settings	A named list (with fields fw and rev) containing the relaxed settings for designing forward/reverse primers. By default (NULL), the relaxed settings are not shown in the report.
...	required.cvg (optional, default: 1), the desired coverage ratio if primers is a single primer set.

Value

write_templates stores templates to fname.

write_primers stores primers to disk.

create_coverage_xls stores information on the primer coverage in a spreadsheet.

create_report Creates a PDF file summarizing the results from analyzing one or multiple sets of primers.

write_settings returns the status from closing the connection to the output file.

Note

Creating the report requires the external programs Pandoc (http://pandoc.org) and LaTeX (http://latex-project.org).

Examples

data(Ippolito)
# Store templates as FASTA
fname.fasta <- tempfile("my_templates", fileext = ".fasta")
write_templates(template.df, fname.fasta)
# Store templates as CSV
fname.csv <- tempfile("my_templates", fileext = ".csv")
write_templates(template.df, fname.csv, "CSV")

data(Ippolito)
# Store primers as FASTA
fname.fasta <- tempfile("my_primers", fileext = ".fasta")
write_primers(primer.df, fname.fasta)
# Store primers as CSV
fname.csv <- tempfile("my_primers", fileext = ".csv")
write_primers(primer.df, fname.csv, "CSV")

data(Ippolito)
filename <- tempfile("cvg_overview", fileext = ".xls")
# Store coverage of a single primer in an XLS file:
my.primers <- primer.df[3,]
cvd <- unique(unlist(strsplit(my.primers$Covered_Seqs, split = ",")))
m <- match(cvd, template.df$Identifier)
my.templates <- template.df[m,]
create_coverage_xls(my.primers, my.templates, filename, settings)

setting.xml <- system.file("extdata", "settings", 
                 "C_Taq_PCR_high_stringency.xml", package = "openPrimeR")
settings <- read_settings(setting.xml)
# Creation of a report for a single primer set
data(Ippolito)
out.file.single <- tempfile("evaluation_report", fileext = ".pdf")
create_report(primer.df, template.df, out.file.single, settings)
# Creation of a report for multiple primer sets
data(Comparison)
set.sizes <- sapply(primer.data, nrow)
sel.sets <- order(set.sizes)[1:2]
out.file.comp <- tempfile("comparison_report", fileext = ".pdf")
create_report(primer.data[sel.sets], template.data[sel.sets], out.file.comp, settings)

# Store settings to disk
xml <- system.file("extdata", "settings", 
       "C_Taq_PCR_high_stringency.xml", package = "openPrimeR")
settings <- read_settings(xml)
out.file <- tempfile("my_settings", fileext = ".xml")
write_settings(settings, out.file)

matdoering/openPrimeR documentation built on Feb. 11, 2024, 9:22 p.m.