R/strvalidator-package.r

In strvalidator: Process Control and Validation of Forensic STR Kits

#' @title Process Control and Internal Validation of Forensic STR Kits
#' @docType package
#' @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 kit.
#' Its graphical user interface simplifies the analysis of data exported from e.g.
#' GeneMapper software, without extensive knowledge about R. It provides
#' functions to import, view, edit, and export data. After analysis the results,
#' generated plots, heat-maps, and data can be saved in a project for easy access.
#' Currently, 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 the GeneMapper bins- and panels files.
#' EPG like plots can be generate from data. STR-validator can greatly increase the speed of
#' validation by reducing the time and effort needed to analyze the 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 and is maintained by Oskar Hansson, senior forensic
#' scientist at Oslo University Hospital (OUS), Section for Forensic Biology.
#' 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 is now performed as
#' a 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 at 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}
#'
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#' ESX17 Positive Control Profile
#'
#' A dataset in 'GeneMapper' format containing the DNA profile of
#' the ESX17 positive control sample with homozygotes as one entry.
#'
#' @docType data
#' @keywords datasets
#' @name ref1
#' @usage data(ref1)
#' @format A data frame with 17 rows and 4 variables
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#' SGMPlus example data
#'
#' A slimmed reference dataset containing an arbitrary SGMPlus DNA profile.
#'
#' @docType data
#' @keywords datasets
#' @name ref2
#' @usage data(ref2)
#' @format A data frame with 16 rows and 3 variables
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#' ESX17 Positive Control Profile
#'
#' A dataset in 'GeneMapper' format containing the DNA profile of
#' the ESX17 positive control sample with homozygotes as two entries.
#'
#' @docType data
#' @keywords datasets
#' @name ref11
#' @usage data(ref11)
#' @format A data frame with 17 rows and 4 variables
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#' Typing data in 'GeneMapper' format
#'
#' A dataset containing ESX17 genotyping result for 8 replicates
#' of the positive control sample, a negative control and ladder.
#'
#' @docType data
#' @keywords datasets
#' @name set1
#' @usage data(set1)
#' @format A data frame with 170 rows and 13 variables
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#' SGMPlus example data
#'
#' A slimmed dataset containing SGM Plus genotyping result for 2 replicates
#' of 'sampleA'.
#'
#' @docType data
#' @keywords datasets
#' @name set2
#' @usage data(set2)
#' @format A data frame with 32 rows and 5 variables
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#' ESX17 example data for dropout analysis.
#'
#' Data from dilution experiment for dropout analysis.
#' Text file with exported GeneMapper genotypes table.
#'
#' @docType data
#' @keywords datasets
#' @name set3
#' @format ASCII text file
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#' ESX17 example data for dropout analysis.
#'
#' Reference profiles for source samples.
#' Text file in GeneMapper format.
#'
#' @docType data
#' @keywords datasets
#' @name ref3
#' @format ASCII text file
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#' ESX17 example data for dropout analysis.
#'
#' A slimmed dataset containing data from
#' dilution experiment for dropout analysis (from set3).
#' One sample replicate has lower case sample name (bc9).
#'
#' @docType data
#' @keywords datasets
#' @name set4
#' @usage data(set4)
#' @format A data frame with 1609 rows and 5 variables
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#' 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 lower case sample name.
#'
#' @docType data
#' @keywords datasets
#' @name ref4
#' @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
#' mixture experiment for Mx analysis.
#'
#' @docType data
#' @keywords datasets
#' @name set5
#' @usage data(set5)
#' @format A data frame with 1663 rows and 7 variables
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#' ESX17 example data for mixture analysis.
#'
#' A slimmed dataset containing the reference profile for the major
#' component  in set5.
#'
#' @docType data
#' @keywords datasets
#' @name ref51
#' @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.
#'
#' @docType data
#' @keywords datasets
#' @name ref52
#' @usage data(ref52)
#' @format A data frame with 34 rows and 3 variables
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#' Fusion example data for dropout analysis.
#'
#' A slimmed dataset containing data from
#' sensitivity experiment for dropout analysis.
#'
#' @docType data
#' @keywords datasets
#' @name set6
#' @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.
#'
#' @docType data
#' @keywords datasets
#' @name ref61
#' @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 same as set6.
#' NB! Reference R has a Y marker with NA.
#'
#' @docType data
#' @keywords datasets
#' @name ref62
#' @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
#' inhibition experiment.
#'
#' @docType data
#' @keywords datasets
#' @name set7
#' @usage data(set7)
#' @format A data frame with 883 rows and 7 variables
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#' ESSplex SE QS example data for inhibition analysis.
#'
#' A slimmed dataset containing the reference profile for the
#' samples in set7.
#'
#' @docType data
#' @keywords datasets
#' @name ref7
#' @usage data(ref7)
#' @format A data frame with 35 rows and 4 variables
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