Input {openPrimeR} | R Documentation

## Input Functionalities.

### Description

`read_primers`

  Reads one or multiple input files with primer sequences. The input can either be in FASTA or in CSV format.

`read_templates`

  Read one or multiple files with template sequences in FASTA or CSV format.

`read_settings`

  Loads primer analysis settings from an XML file.

`Templates`

  The `Templates` class encapsulates a data frame containing the sequencs of the templates, their binding regions, as well as additional information (e.g. template coverage).

`Primers`

  The `Primers` class encapsulates a data frame representing a set of primers. Objects of this class store all properties associated with a set of primers, for example the results from evaluating the properties of a primer set or from determining its coverage.

### Usage

    Templates(...)

    read_templates(fname, hdr.structure = NULL, delim = NULL,
      id.column = NULL, rm.keywords = NULL, remove.duplicates = FALSE,
      fw.region = c(1, 30), rev.region = c(1, 30), gap.char = "-",
      run = NULL)

    Primers(...)

    read_primers(fname, fw.id = "_fw", rev.id = "_rev",
      merge.ambig = c("none", "merge", "unmerge"), max.degen = 16,
      template.df = NULL, adapter.action = c("warn", "rm"),
      sample.name = NULL, updateProgress = NULL)

    read_settings(filename = list.files(system.file("extdata", "settings", package
      = "openPrimeR"), pattern = "*.xml", full.names = TRUE), frontend = FALSE)

### Arguments

`...` | A data frame fulfilling the structural requirements for initializing a `Templates` or `Primers` object.
`fname` | Character vector providing either a single or multiple paths to FASTA or CSV files.
`hdr.structure` | A character vector describing the information contained in the FASTA headers. In case that the headers of `fasta.file` contain template group information, please include the keyword "GROUP" in `hdr.structure`. If the numer of elements provided via `hdr.structure` is shorter than the actual header structure, the missing fields are ignored.
`delim` | Delimiter for the information in the FASTA headers.
`id.column` | Field in the header to be used as the identifier of individual template sequences.
`rm.keywords` | A vector of keywords that are used to remove templates whose headers contain any of the keywords.
`remove.duplicates` | Whether duplicate sequence shall be removed.
`fw.region` | The positional interval from the template 5' end specifying the binding sites for forward primers. The default `fw.region` is set to the first 30 bases of the templates.
`rev.region` | The positional interval from the template 3' end specifying the binding sites for reverse primers. The default `rev.region` is set to the last 30 bases of the templates.
`gap.char` | The character in the input file representing gaps. Gaps are automatically removed upon input and the default character is "-".
`run` | An identifier for the set of template sequences. By default, `run` is `NULL` and its value is set via `template.file`.
`fw.id` | For FASTA input, the identifier for forward primers in the FASTA headers.
`rev.id` | For FASTA input, the identifier for reverse primers in the FASTA headers.
`merge.ambig` | Indicates whether similar primers should be merged ("merge") using IUPAC ambiguity codes or whether primers should be disambiguated ("unmerge"). By default `merge.ambig` is set to "none", leaving primers as they are.
`max.degen` | A scalar numeric providing the maximum allowed degeneracy for merging primers if `merge.ambig` is set to "merge". Degeneracy is defined by the number of disambiguated sequences that are represented by a degenerate primer.
`template.df` | An object of class `Templates`. If `template.df` is provided for `read_primers` then the primers are checked for restriction sites upon input; otherwhise they are not checked.
`adapter.action` | The action to be performed when `template.df` is provided for identifying adapter sequences. Either "warn" to issue warning about adapter sequences or "rm" to remove identified adapter sequences. The default is "warn".
`sample.name` | An identifier for the input primers.
`updateProgress` | A Shiny progress callback function. This is `NULL` by default such that no progress is tracked.
`filename` | Path to a valid XML file containing the primer analysis settings. By default, `filename` is set to all settings that are shipped with openPrimeR and the lexicographically first file is loaded.
`frontend` | Indicates whether settings shall be loaded for the Shiny frontend. In this case no unit conversions for the PCR settings are performed. The default setting is `FALSE` such that the correct units are used.

### Details

In the following you can find a description of the most important columns that can be found in an object of class `Templates`. Note that angle brackets in the column names indicate the existence of multiple possibilities.

`ID`

  The identifiers of the templates.

`Identifier`

  The internal identifiers of the templates.

`Group`

  The identifiers of the groups that the templates belong to.

`Allowed_Start_<fw|rev>`

  The start of the interval in the templates where binding is allowed for forward and reverse primers, respectively.

`Allowed_End_<fw|rev>`

  The end of the interval in the templates where binding is allowed for forward and reverse primers, respectively.

`Allowed_<fw|rev>`

  The template sequence where binding is allowed for forward and reverse primers, respectively.

`Run`

  An identifier for the set of template sequences.

`Covered_By_Primers`

  The identifiers of primers covering the templates, when the template coverage has been annotated.

`primer_coverage`

  The number of primers covering the templates, when the template coverage has been annotated.

When loading a FASTA file with `read_templates`, the input arguments `hdr.structure`, `delim`, `id.column`, `rm.keywords`, `remove.duplicates`, `fw.region`, `rev.region`, `gap.character`, and `run` are utilized. Most importantly, `hdr.structure` and `delim` should match the FASTA header structure. To learn more about setting the primer binding regions, consider the `assign_binding_regions` function. In contrast, when a CSV file is loaded with `read_templates`, the data are loaded without performing any modifications because the CSV file should represent an object of class `Templates`, which can be stored using the `write_templates` function.

When loading primers via `read_primers`, the input arguments `fw.id`, `rev.id`, `merge.ambig`, and `max.degen` are only used for loading primers from a FASTA file. In this case, please ensure that `fw.id` and `rev.id` are set according to the keywords indicating the primer directionalities in the FASTA file. When loading primers from a CSV file, the format of the file should adhere to the structure defined by the `Primers` class.

When loading a settings file with `read_settings`, if `filename` is not provided, a default XMl settings file is loaded. Please review the function's examples to learn more about the default settings. If you want to load custom settings, you can store a modified `DesignSettings` object as an XML file using `write_settings`.

### Value

The `Templates` constructor returns a `Templates` object, an instance of a data frame.

`read_templates` returns a single object of class `Templates` if a single filename was provided or a list of such objects if multiple file names were provided.

The `Primers` constructor returns an object of class `Primers`.

`read_primers` returns a single object of class `Primers` if a single input file is provided or a list of such objects if multiple files are provided.

`read_settings` returns an object of class `DesignSettings`.

### Basic columns

In the following you can find a description of the most important columns that can be found in objects of class `Primers`. Note that angular brackets indicate the existence of multiple possibilities. The following columns are present when a set of primers is loaded from a FASTA file using `read_primers`:

`ID`

  The identifiers of the primers.

`Identifier`

  The internal identifiers of the primers.

`Forward`

  The sequences of forward primers.

`Reverse`

  The sequences of reverse primers.

`primer_length<fw|rev>`

  The lengths of forward and reverse primer sequences, respectively.

`Direction`

  Either 'fw' for forward primers, 'rev' for reverse primers, or 'both' for a primer pair.

`Degeneracy_<fw|rev>`

  The degeneracy (ambiguity) of forward and reverse primers, respectively.

`Run`

  An identifier describing the primer set.

### Coverage-related columns

The following columns are only available in an object of class `Primers` after primer coverage has been computed, that is after `check_constraints` has been called with the active `primer_coverage` constraint. Computed coverage values relating solely to string matching are indicated by the prefix `Basic_`, while columns without this prefix relate to the coverage after applying the constraints formulated via `CoverageConstraints`. Information on off-target coverage events are indicated by the `Off_` prefix, while on-target coverage events do not carry this prefix.

`primer_coverage`

  The number of templates that are covered by the primers. Note that if a primer set contains primers of both directions, a template is only considered covered if it is covered by primers of both directions.

`Coverage_Ratio`

  The ratio of templates that are covered by the primers.

`Binding_Position_Start_<fw|rev>`

  The upstream position in the templates where forward and reverse primers respectively bind.

`Binding_Position_End_<fw|rev>`

  The downstream position in the templates where forward and reverse primers respectively bind.

`Relative_<Forward|Reverse>_Binding_Position_<Start|End>_<fw|rev>`

  The binding upstream (`Start`) or downstream (`End`) positions of the primers relative to the forward (`Forward`) or reverse (`Reverse`) binding regions, either for forward (`fw`) or reverse primers (`rev`).

`Binding_Region_Allowed`

  Whether a coverage event occurred in the target binding region or not. If the allowed off-target ratio was set to 0 only coverage events within the the target region are reported.

`Nbr_of_mismatches_<fw|rev>`

  The number of mismatches of forward and reverse primer coverage events, respectively.

`Mismatch_pos_<fw|rev>`

  The position of mismatches for forward and reverse coverage events, respectively. Mismatch positions are reported relative to the 3' end, that is, position 1 indicates a mismatch in the last base of a primer.

`primer_specificity`

  The specificity of a primer as determined by its ratio of off-target binding events.

### Constraint-related columns

Each constraint that is considered when calling `check_constraints` gives rise to at least one column in the provided `Primers` object. Due to the large number of possible constraints, we will limit our description to the `gc_clamp` constraint. Once the GC clamp property has been computed, the `gc_clamp_fw` column contains the length of the GC clamp for forward primers and `gc_clamp_rev` the corresponding length for reverse primers. Whether the desired extent of the GC clamp was obtained by a primer is indicated by the `EVAL_gc_clamp` column. It contains `TRUE` when the GC clamp constraint was fulfilled and `FALSE` when it was broken. To identify whether all required constraints were fulfilled by a primer, the `constraints_passed` column can be used. It contains `TRUE` if all `active.constraints` used by `check_constraints` were fulfilled and `FALSE` otherwise.

### Examples

    # Load a set of templates:
    fasta.file <- system.file("extdata", "IMGT_data", "templates",
         "Homo_sapiens_IGH_functional_exon.fasta", package = "openPrimeR")
    hdr.structure <- c("ACCESSION", "GROUP", "SPECIES", "FUNCTION")
    template.df <- read_templates(fasta.file, hdr.structure, "|", "GROUP")
    # Load templates from a FASTA file
    fasta.file <- system.file("extdata", "IMGT_data", "templates",
              "Homo_sapiens_IGH_functional_exon.fasta", package = "openPrimeR")
    hdr.structure <- c("ACCESSION", "GROUP", "SPECIES", "FUNCTION")
    template.df.fasta <- read_templates(fasta.file, hdr.structure, "|", "GROUP")
    # Load mutliple FASTA files
    fasta.files <- c(fasta.file, fasta.file)
    template.df.fastas <- read_templates(fasta.files, hdr.structure, "|", "GROUP")
    # Load templates from a previously stored CSV file
    csv.file <- system.file("extdata", "IMGT_data", "comparison",
                   "templates", "IGH_templates.csv", package = "openPrimeR")
    template.df.csv <- read_templates(csv.file)
    # Load multiple CSV files:
    csv.files <- c(csv.file, csv.file)
    template.df.csvs <- read_templates(csv.files)
    # Load a mixture of FASTA/CSV files:
    mixed.files <- c(csv.file, fasta.file)
    template.data <- read_templates(mixed.files)

    # Load a set of primers
    primer.location <- system.file("extdata", "IMGT_data", "primers", "IGHV",
                         "Ippolito2012.fasta", package = "openPrimeR")
    primer.df <- read_primers(primer.location, "_fw", "_rev")

    primer.fasta <- system.file("extdata", "IMGT_data", "primers", "IGHV",
                         "Ippolito2012.fasta", package = "openPrimeR")
    primer.df <- read_primers(primer.fasta, "_fw", "_rev")
    # Read multiple FASTA files
    fasta.files <- list.files(system.file("extdata", "IMGT_data", "primers",
                     "IGHV", package = "openPrimeR"), pattern = "*\\.fasta",
                     full.names = TRUE)[1:3]
    primer.data <- read_primers(fasta.files)
    # Read primers from a CSV file
    primer.csv <- system.file("extdata", "IMGT_data", "comparison",
                 "primer_sets", "IGL", "IGL_openPrimeR2017.csv",  package = "openPrimeR")
    primer.df <- read_primers(primer.csv)
    # Read multiple primer CSV files
    primer.files <- list.files(path = system.file("extdata", "IMGT_data", "comparison",
                             "primer_sets", "IGH", package = "openPrimeR"),
                              pattern = "*\\.csv", full.names = TRUE)[1:3]
    primer.data <- read_primers(primer.files)
    # Read a mixture of FASTA/CSV files:
    mixed.primers <- c(primer.fasta, primer.csv)
    primer.data <- read_primers(mixed.primers)

    # Select available settings
    available.settings <- list.files(
         system.file("extdata", "settings", package = "openPrimeR"),
         pattern = "*.xml", full.names = TRUE)
    # Select one of the settings and load them
    filename <- available.settings[1]
    settings <- read_settings(filename)

[Package openPrimeR version 1.8.0 Index]