AnalysisStats: Primer Analysis Statistics.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

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])

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