AnalysisStats {openPrimeR} | R Documentation

## Primer Analysis Statistics.

### Description

`get_cvg_ratio`

  Determines the ratio of template sequences that are covered by the evaluated input primers. The ratio is in the interval [0,1] where 0 indicates 0% coverage (no templates covered) and 1 indicates 100% coverage (all templates covered).

`get_cvg_stats`

  Retrieve statistics on covered templates, either for a single or multiple primer sets.

`get_cvg_stats_primer`

  Creates a table summarizing the coverage events of individual primers.

`get_comparison_table`

  Creates an overview of the properties of multiple primer sets by providing the inter-quartile range of primer properties in bracket notation.

### Usage

    get_cvg_ratio(primer.df, template.df, allowed.mismatches = NULL,
      cvg.definition = c("constrained", "basic"), mode.directionality = NULL,
      as.char = FALSE)

    get_comparison_table(templates, primers, sample.name = NULL)

    get_cvg_stats_primer(primer.df, template.df, cvg.definition = c("constrained",
      "basic"))

    get_cvg_stats(primers, templates, for.viewing = FALSE,
      total.percentages = FALSE, allowed.mismatches = Inf,
      cvg.definition = c("constrained", "basic"))

### Arguments

`primer.df` | A `Primers` object containing the primers.
`template.df` | A `Templates` object containing the template sequences corresponding to `primer.df`.
`allowed.mismatches` | The number of allowed mismatches for determining the coverage of the templates. By default, all annotated coverage events are considered.
`cvg.definition` | If `cvg.definition` is set to "constrained", the statistics for the expected coverage (after applying the coverage constraints) are retrieved. If `cvg.definition` is set to "basic", the coverage is determined solely by string matching (i.e. without applying the coverage constraints). By default, `cvg.definition` is set to "constrained".
`mode.directionality` | If `mode.directionality` is provided, the coverage of templates is computed for a specific direction of primers. Either "fw" (forward coverage only), "rev" (reverse coverage only), or "both" for both directions. By default, `mode.directionality` is `NULL` such that the directionality of the primers is determined automatically.
`as.char` | Whether the coverage ratio should be outputted as a percentage-formatted character vector. By default, `as.char` is set to `FALSE` such that a numeric is returned.
`templates` | If `primers` is an object of class `Primers`, please provide an object of class `Templates` containing the template sequences targeted by `primers`. If `primers` is a list, `templates` should be a list of `Template` objects.
`primers` | To retrieve statistics for a single primer set, please provide an object of class `Primers` containing a set of evaluated primers. To retrieve statistics for multiple primer sets, pelase provide a list with evaluated `Primers` objects.
`sample.name` | Either a single identifier or a character vector of identifiers for every `Templates` object in `templates`. By default, `sample.name` is `NULL` such that the `Run` annotations in the provided `Templates` objects are used.
`for.viewing` | Whether the table should be formatted to be human-readable. By default, `for.viewing` is `FALSE`.
`total.percentages` | Whether group coverage percentages should be computed in relation to the total number of template sequences or in relation to the number of templates belonging to a specific group. By default, `total.percentages` is `FALSE` suc that the percentages are group-specific.

### Details

The manner in which `get_cvg_ratio` determines the coverage ratio depends on the directionality of the input primers. If either only forward or reverse primers are inputted, the individual coverage of each primer is used to determine the overall coverage. If, however, forward and reverse primers are inputted at the same time, the coverage is defined by the intersection of binding events from both, forward and reverse primers.

For `get_cvg_stats_primer`, the cells corresponding to columns with numeric identifiers indicate the percentage of coverage events occurring with a certain number of mismatches. For example column `3` provides the number of coverage events where there are exactly three mismatches between primers and templates. The column `Group_Coverage` provides a listing of the percentage of covered templates per group.

### Value

By default, `get_cvg_ratio` returns a numeric providing the expected primer coverage ratio. If `as.char` is `TRUE`, the output is provided as a percentage-formatted character vector. The attributes `no_covered`, `no_templates`, and `covered_templates` provide the number of covered templates, the total number of templates, and the IDs of covered templates, respectively.

`get_comparison_table` returns a data frame summarizing the properties of the provided primer data sets.

`get_cvg_stats_primer` returns a list with the following entries. `cvg_per_nbr_mismatches` contains a data frame listing the number of binding events broken down according to the number of expected mismatches between primers and templates. `cvg_per_group` contains a data frame listing the the coverage of individual primers per group of templates.

`get_cvg_stats` returns a data frame whose entries provide the coverage of templates per group of templates.

### Examples

    data(Ippolito)
    # Determine the overall coverage
    cvg.ratio <- get_cvg_ratio(primer.df, template.df)
    # Determine the identitity coverage ratio
    cvg.ratio.0 <- get_cvg_ratio(primer.df, template.df, allowed.mismatches = 0)

    # Summarize the properties of multiple primer sets
    data(Comparison)
    tab <- get_comparison_table(template.data[1:3], primer.data[1:3], "IGH")

    data(Ippolito)
    # Determine coverage stats per primer
    primer.cvg.stats <- get_cvg_stats_primer(primer.df, template.df)

    # Coverage statistics for a single primer set
    data(Ippolito)
    cvg.stats <- get_cvg_stats(primer.df, template.df)
    # Coverage statistics for multiple primer sets
    data(Comparison)
    cvg.stats.comp <- get_cvg_stats(primer.data[1:2], template.data[1:2])

[Package openPrimeR version 1.8.0 Index]