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strvalidator

strvalidator is a package developed for validation and process control of methods and instruments in a forensic genetic laboratory. The graphical user interface STR-validator make it easy to analyse data in accordance with European Network of Forensic Science Institutes (ENFSI) and Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines.

In order to assure correct results, most of the core functions are extensively validated using the 'testthat' package before a new version is released (see STR-validator webpage for details).

STR-validator is a product of the PhD work performed by Oskar Hansson (thesis available at the STR-validator website), which was partly funded by the European Union seventh Framework Programme (FP7/2007-2013) under grant agreement no 285487 (EUROFORGEN-NoE).

Please cite STR-validator as: Hansson O, Gill P, Egeland T (2014). "STR-validator: An open source platform for validation and process control" Forensic Science International: Genetics, 13, 154-166. doi: 10.1016/j.fsigen.2014.07.009

Contributions to the strvalidator package or user community is more than welcome. Contact the developer to:

  • improve existing functionality or add new
  • translate course material, manuals, or tutorial
  • collaborate to implement new functions
  • add tests to validate functions

Created and maintained by: Oskar Hansson, Forensic Genetics (Oslo University Hospital, Norway)

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

464

Version

2.4.0

License

GPL-2

Maintainer

Oskar Hansson

Last Published

September 23rd, 2022

Functions in strvalidator (2.4.0)

calculateAT

Calculate Analytical Threshold
calculateAT6_gui

Calculate Analytical Threshold
calculateCapillary

Calculate Capillary Balance
calculateAllT_gui

Calculate Stochastic Thresholds
calculateAT6

Calculate Analytical Threshold
calculateAllele

Calculate Allele
calculateAllT

Calculate Stochastic Thresholds
calculateAllele_gui

Calculate Allele
calculateAT_gui

Calculate Analytical Threshold
calculateCopies_gui

Calculate Allele Copies
calculateDropout_gui

Calculate Dropout Events
calculateDropout

Calculate Drop-out Events
calculateCapillary_gui

Calculate Capillary Balance
calculateCopies

Calculate Allele Copies
calculateHb

Calculate Heterozygote Balance
calculateLb

Calculate Inter-locus Balance
calculateHb_gui

Calculate Heterozygote Balance
calculateOverlap

Calculate Bins Overlap
calculateOverlap_gui

Calculate Bins Overlap
calculatePullup_gui

Calculate Spectral Pull-up
calculateConcordance_gui

Calculate Concordance
calculateSlope

Calculate Profile Slope.
calculateMixture

Calculate Mixture.
calculateRatio

Calculate Ratio
calculateConcordance

Calculate Concordance.
calculateLb_gui

Calculate Locus Balance
calculatePullup

Calculate Spectral Pull-up
calculateOL

Analyze Off-ladder Alleles
calculateStutter_gui

Calculate Stutter
calculateSlope_gui

Calculate Profile Slope
calculateMixture_gui

Calculate Mixture
calculateRatio_gui

Calculate Ratio
calculateStutter

Calculate Stutter
calculateOL_gui

Analyze Off-ladder Alleles
calculateSpike

Detect Spike
calculateSpike_gui

Detect Spike
cropData_gui

Crop Or Replace
calculateT

Calculate Stochastic Threshold
checkSubset

Check Subset
combine_gui

Combine Datasets
checkDataset

Check Dataset
combineBinsAndPanels

Combine Bins And Panels Files.
colConvert

Convert Columns
calculatePeaks

Calculate Peaks
calculatePeaks_gui

Calculate Peaks
calculateHeight_gui

Calculate Peak Height
export_gui

Export
checkSubset_gui

Check Subset
calculateHeight

Calculate Peak Height.
calculateResultType

Calculate Result Type
filterProfile

Filter Profile
generateEPG_gui

Generate EPG
editData_gui

Edit or View Data Frames
filterProfile_gui

Filter Profile
colNames

Column Names
guessProfile

Guess Profile
export

Export
calculateResultType_gui

Calculate Result Type
generateEPG

Generate EPG
plotEPG2_gui

Plot EPG
plotGroups_gui

Plot Empirical Cumulative Distributions
heightToPeak

Height To Peak.
calculateStatistics_gui

Calculate Statistics
columns

Column Actions
columns_gui

Column Actions
import

Import Data
calculateStatistics

Summary Statistics
detectKit

Detect Kit
getDb

Get Allele Frequency Database
getStrings

Get Language Strings
ggsave_gui

Save Image
makeKit_gui

Make Kit
guessProfile_gui

Guess Profile
plotBalance_gui

Plot Balance
plotCapillary_gui

Plot Capillary Balance
modelDropout_gui

Model And Plot Drop-out Events
plotKit_gui

Plot Kit Marker Ranges
ref1

ESX17 Positive Control Profile
plotAT_gui

Plot Analytical Threshold
plotContamination_gui

Plot Contamination
plotPeaks_gui

Plot Peaks
maskAT

Mask And Prepare Data To Analyze Analytical Threshold
readBinsFile

Read Bins file
plotRatio_gui

Plot Ratio
ref11

ESX17 Positive Control Profile
readPanelsFile

Read Panels File
removeSpike_gui

Remove Spike
import_gui

Import Data
listObjects

List Objects
removeSpike

Remove Spikes
plotPullup_gui

Plot Pull-up
plotPrecision_gui

Plot Precision
plotDropout_gui

Plot Drop-out Events
getKit

Get Kit
getSetting

Get Settings.
ref62

Fusion example data for dropout analysis.
ref52

ESX17 example data for mixture analysis.
plotStutter_gui

Plot Stutter
removeArtefact

Remove Artefacts
scrambleAlleles

Scramble Alleles
ref2

SGMPlus example data
strvalidator

Graphical User Interface For The STR-validator Package
plotEPG2

plotEPG2
plotDistribution_gui

Plot Distribution
sample_tableToList

sample_tableToList
plotSlope_gui

Plot Profile Slope
set2

SGMPlus example data
ref3

ESX17 example data for dropout analysis.
ref7

ESSplex SE QS example data for inhibition analysis.
ref61

Fusion example data for dropout analysis.
set1

Typing data in 'GeneMapper' format
set3

ESX17 example data for dropout analysis.
removeArtefact_gui

Remove Artefact
plotResultType_gui

Plot Result Type
ref4

ESX17 example data for dropout analysis.
set6

Fusion example data for dropout analysis.
trim

Trim Data
sortMarker

Sort Markers
set7

ESSplex SE QS example data for inhibition analysis.
saveObject

Save Object
set4

ESX17 example data for dropout analysis.
set5

ESX17 example data for mixture analysis.
strvalidator-package

Process Control and Internal Validation of Forensic STR Kits
ref51

ESX17 example data for mixture analysis.
slim

Slim Data Frames
slim_gui

Slim Data Frames
trim_gui

Trim Data
addMarker

Add Missing Markers.
addOrder

Add Marker Order.
addSize

Add Size Information.
addDye_gui

Add Dye Information
addData_gui

Add Data
addColor

Add Color Information.
addData

Adds New Data Columns to a Data Frame
auditTrail

Log Audit Trail.
addMarker_gui

Add Missing Markers
addSize_gui

Add Size Information