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strvalidator

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 analyse 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 analyse 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 is written and maintained by Oskar Hansson, senior forensic scientist at the Norwegian Institute of Public Health (NIPH), Department of Forensic Biology. The work has 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 NIPH, and on personal spare time.

More information can be found at: https://sites.google.com/site/forensicapps/strvalidator

Info and user community at Facebook: https://www.facebook.com/pages/STR-validator/240891279451450?ref=tn_tnmn https://www.facebook.com/groups/strvalidator/

The source code is hosted at GitHub: https://github.com/OskarHansson/strvalidator

Please report bugs to: https://github.com/OskarHansson/strvalidator/issues

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Version

Install

install.packages('strvalidator')

Monthly Downloads

265

Version

1.9.0

License

GPL-2

Maintainer

Oskar Hansson

Last Published

March 8th, 2017

Functions in strvalidator (1.9.0)

addSize_gui

Add Size Information
calculateAT

Calculate Analytical Threshold
calculateAT6

Calculate Analytical Threshold
calculateAT6_gui

Calculate Analytical Threshold
calculateHeight_gui

Calculate Peak Height
calculateLb

Calculate Inter-locus Balance
calculatePeaks_gui

Calculate Peaks
calculatePullup

Calculate Spectral Pull-up
calculateSlope_gui

Calculate Profile Slope
calculateSpike

Detect Spike
checkSubset

Check Subset
checkSubset_gui

Check Subset
export_gui

Export
filterProfile

Filter Profile
addOrder

Add Marker Order.
addSize

Add Size Information.
calculateConcordance_gui

Calculate Concordance
calculateCopies

Calculate Allele Copies
calculateCopies_gui

Calculate Allele Copies
calculateDropout

Calculate Drop-out Events
calculateOL_gui

Analyse Off-ladder Alleles
calculateOverlap

Calculate Bins Overlap
heightToPeak

Height To Peak.
import

Import Data
plotPullup_gui

Plot Pull-up
plotRatio_gui

Plot Ratio
ref11

ESX17 Positive Control Profile
calculateRatio_gui

Calculate Ratio
calculateResultType

Calculate Result Type
colConvert

Convert Columns
colNames

Column Names
ref2

SGMPlus example data
removeSpike_gui

Remove Spike
saveObject

Save Object
set4

ESX17 example data for dropout analysis.
set5

ESX17 example data for mixture analysis.
sortMarker

Sort Markers
strvalidator-package

Process Control and Internal Validation of Forensic STR Kits
filterProfile_gui

Filter Profile
generateEPG

Generate EPG
import_gui

Import Data
listObjects

List Objects
plotContamination_gui

Plot Contamination
plotDistribution_gui

Plot Distribution
ref3

ESX17 example data for dropout analysis.
ref4

ESX17 example data for dropout analysis.
ref61

Fusion example data for dropout analysis.
ref62

Fusion example data for dropout analysis.
scrambleAlleles

Scramble Alleles
set1

Typing data in 'GeneMapper' format
tableCapillary_gui

Table Capillary
tablePrecision

Calculate Precision
addData_gui

Add Data
addDye_gui

Add Dye Information
calculateAllele_gui

Calculate Allele
calculateCapillary

Calculate Capillary Balance
calculateDropout_gui

Calculate Dropout Events
calculateHb

Calculate Heterozygote Balance
calculateMixture_gui

Calculate Mixture
addColor

Add Color Information.
addData

Adds New Data Columns to a Data Frame
calculateCapillary_gui

Calculate Capillary Balance
calculateConcordance

Calculate Concordance.
calculateHb_gui

Calculate Heterozygote Balance
calculateHeight

Calculate Peak Height.
calculateOverlap_gui

Calculate Bins Overlap
tableStutter_gui

Table Stutter
trim

Trim Data
calculatePeaks

Calculate Peaks
calculateResultType_gui

Calculate Result Type
calculateSlope

Calculate Profile Slope.
cropData_gui

Crop Or Replace
detectKit

Detect Kit
editData_gui

Edit or View Data Frames
export

Export
calculateOL

Analyse Off-ladder Alleles
calculateStutter_gui

Calculate Stutter
checkDataset

Check Dataset
combineBinsAndPanels

Combine Bins And Panels Files.
addMarker

Add Missing Markers.
combine_gui

Combine Datasets
generateEPG_gui

Generate EPG
getDb

Get Allele Frequency Database
makeKit_gui

Make Kit
maskAT

Mask And Prepare Data To Analyze Analytical Threshold
plotDropout_gui

Plot Drop-out Events
plotKit_gui

Plot Kit Marker Ranges
plotResultType_gui

Plot Result Type
plotSlope_gui

Plot Profile Slope
removeArtefact_gui

Remove Artefact
removeSpike

Remove Spikes
set6

Fusion example data for dropout analysis.
set7

ESSplex SE QS example data for inhibition analysis.
tableBalance_gui

Table Balance
tableCapillary

Table Capillary
guessProfile

Guess Profile
guessProfile_gui

Guess Profile
plotPeaks_gui

Plot Peaks
plotPrecision_gui

Plot Precision
readPanelsFile

Read Panels File
addMarker_gui

Add Missing Markers
calculateAT_gui

Calculate Analytical Threshold
calculateAllele

Calculate Allele
ref1

ESX17 Positive Control Profile
ref51

ESX17 example data for mixture analysis.
ref52

ESX17 example data for mixture analysis.
calculateLb_gui

Calculate Locus Balance
calculateMixture

Calculate Mixture.
calculatePullup_gui

Calculate Spectral Pull-up
calculateRatio

Calculate Ratio
calculateSpike_gui

Detect Spike
slim

Slim Data Frames
slim_gui

Slim Data Frames
tablePrecision_gui

Table Precision
calculateStutter

Calculate Stutter
columns

Column Actions
columns_gui

Column Actions
tableStutter

Table Stutter
trim_gui

Trim Data
getKit

Get Kit
ggsave_gui

Save Image
modelDropout_gui

Model And Plot Drop-out Events
plotAT_gui

Plot Analytical Threshold
plotBalance_gui

Plot Balance
plotCapillary_gui

Plot Capillary Balance
plotStutter_gui

Plot Stutter
readBinsFile

Read Bins file
ref7

ESSplex SE QS example data for inhibition analysis.
removeArtefact

Remove Artefacts
set2

SGMPlus example data
set3

ESX17 example data for dropout analysis.
strvalidator

Graphical User Interface For The STR-validator Package
tableBalance

Table Balance