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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

368

Version

2.3.0

License

GPL-2

Maintainer

Oskar Hansson

Last Published

July 10th, 2020

Functions in strvalidator (2.3.0)

addData

Adds New Data Columns to a Data Frame
addSize_gui

Add Size Information
addDye_gui

Add Dye Information
addOrder

Add Marker Order.
addMarker

Add Missing Markers.
auditTrail

Log Audit Trail.
addData_gui

Add Data
addSize

Add Size Information.
addColor

Add Color Information.
calculateAllele

Calculate Allele
calculateAllele_gui

Calculate Allele
calculateAT_gui

Calculate Analytical Threshold
calculateAT6_gui

Calculate Analytical Threshold
calculateHeight

Calculate Peak Height.
calculateAllT

Calculate Stochastic Thresholds
calculateHb

Calculate Heterozygote Balance
calculatePeaks

Calculate Peaks
calculateAllT_gui

Calculate Stochastic Thresholds
calculateHb_gui

Calculate Heterozygote Balance
calculatePeaks_gui

Calculate Peaks
calculateConcordance

Calculate Concordance.
calculateConcordance_gui

Calculate Concordance
calculateLb

Calculate Inter-locus Balance
calculateStutter

Calculate Stutter
calculateLb_gui

Calculate Locus Balance
calculateCopies

Calculate Allele Copies
getStrings

Get Language Strings
combineBinsAndPanels

Combine Bins And Panels Files.
ggsave_gui

Save Image
combine_gui

Combine Datasets
calculateStutter_gui

Calculate Stutter
calculateCopies_gui

Calculate Allele Copies
calculateCapillary

Calculate Capillary Balance
addMarker_gui

Add Missing Markers
calculateResultType

Calculate Result Type
calculateResultType_gui

Calculate Result Type
calculateCapillary_gui

Calculate Capillary Balance
calculateMixture

Calculate Mixture.
export_gui

Export
colNames

Column Names
calculateAT

Calculate Analytical Threshold
colConvert

Convert Columns
calculateDropout_gui

Calculate Dropout Events
calculateSlope

Calculate Profile Slope.
calculateDropout

Calculate Drop-out Events
calculateSlope_gui

Calculate Profile Slope
calculateMixture_gui

Calculate Mixture
calculateHeight_gui

Calculate Peak Height
import_gui

Import Data
getKit

Get Kit
calculateOverlap

Calculate Bins Overlap
calculateAT6

Calculate Analytical Threshold
calculatePullup_gui

Calculate Spectral Pull-up
calculateOverlap_gui

Calculate Bins Overlap
calculatePullup

Calculate Spectral Pull-up
calculateStatistics_gui

Calculate Statistics
calculateOL

Analyze Off-ladder Alleles
calculateStatistics

Summary Statistics
getSetting

Get Settings.
filterProfile

Filter Profile
calculateRatio

Calculate Ratio
plotPullup_gui

Plot Pull-up
heightToPeak

Height To Peak.
ref61

Fusion example data for dropout analysis.
import

Import Data
plotPrecision_gui

Plot Precision
calculateRatio_gui

Calculate Ratio
readPanelsFile

Read Panels File
ref52

ESX17 example data for mixture analysis.
readBinsFile

Read Bins file
checkSubset

Check Subset
calculateT

Calculate Stochastic Threshold
calculateSpike

Detect Spike
calculateOL_gui

Analyze Off-ladder Alleles
editData_gui

Edit or View Data Frames
checkDataset

Check Dataset
calculateSpike_gui

Detect Spike
set3

ESX17 example data for dropout analysis.
listObjects

List Objects
plotKit_gui

Plot Kit Marker Ranges
set4

ESX17 example data for dropout analysis.
maskAT

Mask And Prepare Data To Analyze Analytical Threshold
plotPeaks_gui

Plot Peaks
export

Export
plotRatio_gui

Plot Ratio
guessProfile

Guess Profile
makeKit_gui

Make Kit
plotResultType_gui

Plot Result Type
checkSubset_gui

Check Subset
cropData_gui

Crop Or Replace
tablePrecision

Calculate Precision
guessProfile_gui

Guess Profile
ref7

ESSplex SE QS example data for inhibition analysis.
tablePrecision_gui

Table Precision
removeArtefact

Remove Artefacts
ref11

ESX17 Positive Control Profile
set1

Typing data in 'GeneMapper' format
ref1

ESX17 Positive Control Profile
trim

Trim Data
trim_gui

Trim Data
ref51

ESX17 example data for mixture analysis.
ref62

Fusion example data for dropout analysis.
ref4

ESX17 example data for dropout analysis.
plotDropout_gui

Plot Drop-out Events
columns

Column Actions
detectKit

Detect Kit
set2

SGMPlus example data
plotGroups_gui

Plot Empirical Cumulative Distributions
strvalidator-package

Process Control and Internal Validation of Forensic STR Kits
saveObject

Save Object
plotBalance_gui

Plot Balance
generateEPG_gui

Generate EPG
columns_gui

Column Actions
strvalidator

Graphical User Interface For The STR-validator Package
filterProfile_gui

Filter Profile
generateEPG

Generate EPG
getDb

Get Allele Frequency Database
set7

ESSplex SE QS example data for inhibition analysis.
tableBalance

Table Balance
removeArtefact_gui

Remove Artefact
slim

Slim Data Frames
tableBalance_gui

Table Balance
scrambleAlleles

Scramble Alleles
plotCapillary_gui

Plot Capillary Balance
modelDropout_gui

Model And Plot Drop-out Events
plotAT_gui

Plot Analytical Threshold
slim_gui

Slim Data Frames
ref2

SGMPlus example data
removeSpike

Remove Spikes
ref3

ESX17 example data for dropout analysis.
plotContamination_gui

Plot Contamination
plotDistribution_gui

Plot Distribution
sortMarker

Sort Markers
plotSlope_gui

Plot Profile Slope
plotStutter_gui

Plot Stutter
tableCapillary

Table Capillary
tableStutter

Table Stutter
tableStutter_gui

Table Stutter
removeSpike_gui

Remove Spike
set5

ESX17 example data for mixture analysis.
set6

Fusion example data for dropout analysis.
tableCapillary_gui

Table Capillary