R/strvalidator-package.r

In OskarHansson/strvalidator: Process Control and Validation of Forensic STR Kits

#' @title Process Control and Internal Validation of Forensic STR Kits
#' @name strvalidator-package
#' @author Oskar Hansson \email{oskhan@@ous-hf.no}
#' @keywords package
#' @description STR-validator is a free and open-source R package intended for
#' process control and internal validation of forensic STR DNA typing kits.
#' Its graphical user interface simplifies the analysis of data exported from
#' software like GeneMapper, without requiring extensive knowledge about R. It provides
#' functions to import, view, edit, and export data. After analysis, the results,
#' generated plots, heatmaps, and data can be saved in a project for easy access.
#' Analysis modules for stutter, balance, dropout, mixture, concordance,
#' typing result, precision, pull-up, and analytical thresholds are available.
#' In addition, there are functions to analyze GeneMapper bins and panels files.
#' EPG-like plots can be generated from data. STR-validator can significantly
#' increase the speed of validation by reducing the time and effort needed to
#' analyze validation data. It allows exploration of the characteristics of DNA
#' typing kits according to ENFSI and SWGDAM recommendations. This facilitates
#' the implementation of probabilistic interpretation of DNA results.
#'
#' STR-validator was written by and is maintained by Oskar Hansson, 
#' Section of Digitalization and Development, Oslo University Hospital (OUS).
#' The work initially received external funding from the European
#' Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no.
#' 285487 (EUROFORGEN-NoE) but development and maintenance are now performed as
#' part of my position at OUS, and on personal spare time.\cr\cr
#'
#' Effort has been made to assure correct results. Refer to the main website
#' for a list of functions specifically tested at build time.\cr\cr
#'
#' Click \code{Index} at the bottom of the page to see a complete list of
#' functions.\cr\cr
#'
#' Created and maintained by:\cr
#' Oskar Hansson, Section for Forensic Biology (OUS, Norway)\cr\cr
#'
#' More information can be found at:\cr
#' \url{https://sites.google.com/site/forensicapps/strvalidator}\cr\cr
#'
#' Info and user community at Facebook:\cr
#' \url{https://www.facebook.com/pages/STR-validator/240891279451450?ref=tn_tnmn}\cr\cr
#' \url{https://www.facebook.com/groups/strvalidator/}\cr\cr
#'
#' The source code is hosted on GitHub:\cr
#' \url{https://github.com/OskarHansson/strvalidator}\cr\cr
#'
#' Please report bugs to:\cr
#' \url{https://github.com/OskarHansson/strvalidator/issues}\cr\cr
#'
#' @references
#' Recommended Minimum Criteria for the Validation of Various Aspects of the DNA Profiling Process
#' \url{http://enfsi.eu/wp-content/uploads/2016/09/minimum_validation_guidelines_in_dna_profiling_-_v2010_0.pdf}
#' Validation Guidelines for Forensic DNA Analysis Methods (2012)
#' \url{http://media.wix.com/ugd/4344b0_cbc27d16dcb64fd88cb36ab2a2a25e4c.pdf}
#'
#' @importFrom stats rnorm
#' @importFrom utils head
"_PACKAGE"

#' ESX17 Positive Control Profile
#'
#' A dataset in 'GeneMapper' format containing the DNA profile of
#' the ESX17 positive control sample with homozygotes as one entry.
#'
#' @name ref1
#' @keywords datasets
#' @usage data(ref1)
#' @format A data frame with 17 rows and 4 variables
NULL

#' SGMPlus Example Data
#'
#' A slimmed reference dataset containing an arbitrary SGMPlus DNA profile.
#'
#' @name ref2
#' @keywords datasets
#' @usage data(ref2)
#' @format A data frame with 16 rows and 3 variables
NULL

#' ESX17 Positive Control Profile
#'
#' A dataset in 'GeneMapper' format containing the DNA profile of
#' the ESX17 positive control sample with homozygotes as two entries.
#'
#' @name ref11
#' @keywords datasets
#' @usage data(ref11)
#' @format A data frame with 17 rows and 4 variables
NULL

#' Typing Data in 'GeneMapper' Format
#'
#' A dataset containing ESX17 genotyping results for 8 replicates
#' of the positive control sample, a negative control, and a ladder.
#'
#' @name set1
#' @keywords datasets
#' @usage data(set1)
#' @format A data frame with 170 rows and 13 variables
NULL

#' SGMPlus Example Data
#'
#' A slimmed dataset containing SGM Plus genotyping results for 2 replicates
#' of 'sampleA'.
#'
#' @name set2
#' @keywords datasets
#' @usage data(set2)
#' @format A data frame with 32 rows and 5 variables
NULL

#' ESX17 Example Data for Dropout Analysis
#'
#' Data from a dilution experiment for dropout analysis.
#' Text file with exported GeneMapper genotypes table.
#'
#' @name set3
#' @keywords datasets
#' @format ASCII text file
NULL

#' ESX17 Example Data for Dropout Analysis
#'
#' Reference profiles for source samples.
#' Text file in GeneMapper format.
#'
#' @name ref3
#' @keywords datasets
#' @format ASCII text file
NULL

#' ESX17 Example Data for Dropout Analysis
#'
#' A slimmed dataset containing data from
#' a dilution experiment for dropout analysis (from set3).
#' One sample replicate has a lower case sample name (bc9).
#'
#' @name set4
#' @keywords datasets
#' @usage data(set4)
#' @format A data frame with 1609 rows and 5 variables
NULL

#' ESX17 Example Data for Dropout Analysis
#'
#' A slimmed dataset containing reference profiles for source samples in set4.
#' Reference 'A2' has double entries for homozygotes.
#' Reference 'F2' has single entries for homozygotes.
#' Reference 'bc' has double entries for homozygotes, and a lower case sample name.
#'
#' @name ref4
#' @keywords datasets
#' @usage data(ref4)
#' @format A data frame with 98 rows and 3 variables
NULL

#' ESX17 Example Data for Mixture Analysis
#'
#' A slimmed dataset containing data from
#' a mixture experiment for Mx analysis.
#'
#' @name set5
#' @keywords datasets
#' @usage data(set5)
#' @format A data frame with 1663 rows and 7 variables
NULL

#' ESX17 Example Data for Mixture Analysis
#'
#' A slimmed dataset containing the reference profile for the major
#' component in set5.
#'
#' @name ref51
#' @keywords datasets
#' @usage data(ref51)
#' @format A data frame with 34 rows and 3 variables
NULL

#' ESX17 Example Data for Mixture Analysis
#'
#' A slimmed dataset containing the reference profile for the minor
#' component in set5.
#'
#' @name ref52
#' @keywords datasets
#' @usage data(ref52)
#' @format A data frame with 34 rows and 3 variables
NULL

#' Fusion Example Data for Dropout Analysis
#'
#' A slimmed dataset containing data from
#' a sensitivity experiment for dropout analysis.
#'
#' @name set6
#' @keywords datasets
#' @usage data(set6)
#' @format A data frame with 1848 rows and 7 variables
NULL

#' Fusion Example Data for Dropout Analysis
#'
#' A slimmed dataset containing the reference profile for the
#' samples in set6.
#' NB! Marker order is different from set6.
#' NB! Reference R has a Y marker with NA.
#'
#' @name ref61
#' @keywords datasets
#' @usage data(ref61)
#' @format A data frame with 89 rows and 3 variables
NULL

#' Fusion Example Data for Dropout Analysis
#'
#' A slimmed dataset containing the reference profile for the
#' samples in set6.
#' NB! Marker order is the same as set6.
#' NB! Reference R has a Y marker with NA.
#'
#' @name ref62
#' @keywords datasets
#' @usage data(ref62)
#' @format A data frame with 89 rows and 3 variables
NULL

#' ESSplex SE QS Example Data for Inhibition Analysis
#'
#' A slimmed dataset containing data from
#' an inhibition experiment.
#'
#' @name set7
#' @keywords datasets
#' @usage data(set7)
#' @format A data frame with 883 rows and 7 variables
NULL

#' ESSplex SE QS Example Data for Inhibition Analysis
#'
#' A slimmed dataset containing the reference profile for the
#' samples in set7.
#'
#' @name ref7
#' @keywords datasets
#' @usage data(ref7)
#' @format A data frame with 35 rows and 4 variables
NULL