Output {openPrimeR} | R Documentation

## 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)

[Package openPrimeR version 1.10.4 Index]