calculatePeaks: Calculate Peaks

In strvalidator: Process Control and Validation of Forensic STR Kits

Calculate Peaks

Description

Calculates the number of peaks in samples.

Usage

calculatePeaks(
  data,
  bins = c(0, 2, 3),
  labels = NULL,
  ol.rm = FALSE,
  by.marker = FALSE,
  debug = FALSE
)

Arguments

data	data frame containing at least the columns 'Sample.Name' and 'Height'.
bins	numeric vector containing the cut-off points defined as maximum number of peaks for all but the last label, which is anything above final cut-off. Must be sorted in ascending order.
labels	character vector defining the group labels. Length must be equal to number of bins + one label for anything above the final cut-off.
ol.rm	logical if TRUE, off-ladder alleles 'OL' peaks will be discarded. if FALSE, all peaks will be included in the calculations.
by.marker	logical if TRUE, peaks will counted per marker. if FALSE, peaks will counted per sample.
debug	logical indicating printing debug information.

Details

Count the number of peaks in a sample profile based on values in the 'Height' column. Each sample is labeled according to custom labels defined by the number of peaks. Peaks can be counted by sample or by marker within a sample. There is an option to discard off-ladder peaks ('OL'). The default purpose for this function is to categorize contamination in negative controls, but it can be used to simply calculating the number of peaks in any sample. NB! A column 'Peaks' for the number of peaks will be created. If present it will be overwritten. NB! A column 'Group' for the sample group will be created. If present it will be overwritten. NB! A column 'Id' will be created by combining the content in the 'Sample.Name' and 'File' column (if available). The unique entries in the 'Id' column will be the definition of a unique sample. If 'File' is present this allows for identical sample names in different batches (files) to be identified as unique samples. If 'Id' is present it will be overwritten.

Value

data.frame with with additional columns 'Peaks', 'Group', and 'Id'.

strvalidator documentation built on July 26, 2023, 5:45 p.m.