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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

333

Version

2.2.0

License

GPL-2

Maintainer

Oskar Hansson

Last Published

March 22nd, 2019

Functions in strvalidator (2.2.0)

addOrder

Add Marker Order.
auditTrail

Log Audit Trail.
colConvert

Convert Columns
calculateAllT

Calculate Stochastic Thresholds
colNames

Column Names
plotDistribution_gui

Plot Distribution
calculateAllT_gui

Calculate Stochastic Thresholds
editData_gui

Edit or View Data Frames
calculateDropout_gui

Calculate Dropout Events
plotContamination_gui

Plot Contamination
ref7

ESSplex SE QS example data for inhibition analysis.
addData_gui

Add Data
export

Export
plotResultType_gui

Plot Result Type
ref4

ESX17 example data for dropout analysis.
calculateAT_gui

Calculate Analytical Threshold
combine_gui

Combine Datasets
calculateHb

Calculate Heterozygote Balance
calculateHb_gui

Calculate Heterozygote Balance
guessProfile

Guess Profile
guessProfile_gui

Guess Profile
calculateCapillary

Calculate Capillary Balance
calculateRatio

Calculate Ratio
addDye_gui

Add Dye Information
calculateLb

Calculate Inter-locus Balance
slim

Slim Data Frames
plotRatio_gui

Plot Ratio
calculateLb_gui

Calculate Locus Balance
calculateCopies

Calculate Allele Copies
calculateCopies_gui

Calculate Allele Copies
calculateRatio_gui

Calculate Ratio
set4

ESX17 example data for dropout analysis.
calculateOverlap_gui

Calculate Bins Overlap
calculateAllele

Calculate Allele
ref51

ESX17 example data for mixture analysis.
set1

Typing data in 'GeneMapper' format
calculateHeight_gui

Calculate Peak Height
calculatePullup

Calculate Spectral Pull-up
calculateAllele_gui

Calculate Allele
set5

ESX17 example data for mixture analysis.
import

Import Data
set2

SGMPlus example data
calculateDropout

Calculate Drop-out Events
calculateOverlap

Calculate Bins Overlap
addColor

Add Color Information.
set7

ESSplex SE QS example data for inhibition analysis.
calculatePullup_gui

Calculate Spectral Pull-up
plotAT_gui

Plot Analytical Threshold
calculateT

Calculate Stochastic Threshold
calculateAT

Calculate Analytical Threshold
checkSubset

Check Subset
calculateAT6_gui

Calculate Analytical Threshold
listObjects

List Objects
addData

Adds New Data Columns to a Data Frame
calculateCapillary_gui

Calculate Capillary Balance
calculateHeight

Calculate Peak Height.
saveObject

Save Object
checkDataset

Check Dataset
ref3

ESX17 example data for dropout analysis.
calculateStutter

Calculate Stutter
plotDropout_gui

Plot Drop-out Events
calculateSlope_gui

Calculate Profile Slope
calculateMixture_gui

Calculate Mixture
calculateMixture

Calculate Mixture.
tablePrecision

Calculate Precision
combineBinsAndPanels

Combine Bins And Panels Files.
set6

Fusion example data for dropout analysis.
calculateSpike_gui

Detect Spike
plotBalance_gui

Plot Balance
tablePrecision_gui

Table Precision
tableStutter_gui

Table Stutter
calculatePeaks_gui

Calculate Peaks
calculatePeaks

Calculate Peaks
cropData_gui

Crop Or Replace
readPanelsFile

Read Panels File
checkSubset_gui

Check Subset
getDb

Get Allele Frequency Database
detectKit

Detect Kit
generateEPG_gui

Generate EPG
heightToPeak

Height To Peak.
import_gui

Import Data
calculateSlope

Calculate Profile Slope.
tableCapillary_gui

Table Capillary
makeKit_gui

Make Kit
calculateStutter_gui

Calculate Stutter
ggsave_gui

Save Image
calculateSpike

Detect Spike
export_gui

Export
getKit

Get Kit
filterProfile

Filter Profile
plotCapillary_gui

Plot Capillary Balance
modelDropout_gui

Model And Plot Drop-out Events
plotSlope_gui

Plot Profile Slope
plotStutter_gui

Plot Stutter
scrambleAlleles

Scramble Alleles
sortMarker

Sort Markers
maskAT

Mask And Prepare Data To Analyze Analytical Threshold
plotKit_gui

Plot Kit Marker Ranges
tableBalance_gui

Table Balance
set3

ESX17 example data for dropout analysis.
plotGroups_gui

Plot Empirical Cumulative Distributions
readBinsFile

Read Bins file
ref2

SGMPlus example data
ref62

Fusion example data for dropout analysis.
addMarker

Add Missing Markers.
slim_gui

Slim Data Frames
removeArtefact

Remove Artefacts
columns_gui

Column Actions
tableCapillary

Table Capillary
removeArtefact_gui

Remove Artefact
calculateConcordance_gui

Calculate Concordance
tableStutter

Table Stutter
plotPeaks_gui

Plot Peaks
calculateConcordance

Calculate Concordance.
strvalidator-package

Process Control and Internal Validation of Forensic STR Kits
ref11

ESX17 Positive Control Profile
tableBalance

Table Balance
ref1

ESX17 Positive Control Profile
addMarker_gui

Add Missing Markers
trim_gui

Trim Data
trim

Trim Data
strvalidator

Graphical User Interface For The STR-validator Package
columns

Column Actions
calculateAT6

Calculate Analytical Threshold
removeSpike_gui

Remove Spike
calculateResultType

Calculate Result Type
plotPrecision_gui

Plot Precision
calculateOL

Analyze Off-ladder Alleles
calculateOL_gui

Analyze Off-ladder Alleles
filterProfile_gui

Filter Profile
calculateResultType_gui

Calculate Result Type
generateEPG

Generate EPG
removeSpike

Remove Spikes
plotPullup_gui

Plot Pull-up
ref52

ESX17 example data for mixture analysis.
ref61

Fusion example data for dropout analysis.
addSize_gui

Add Size Information
addSize

Add Size Information.