Package: qtl 1.70

Karl W Broman

qtl: Tools for Analyzing QTL Experiments

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.

Authors:Karl W Broman [aut, cre], Hao Wu [aut], Gary Churchill [ctb], Saunak Sen [ctb], Danny Arends [ctb], Robert Corty [ctb], Timothee Flutre [ctb], Ritsert Jansen [ctb], Pjotr Prins [ctb], Lars Ronnegard [ctb], Rohan Shah [ctb], Laura Shannon [ctb], Quoc Tran [ctb], Aaron Wolen [ctb], Brian Yandell [ctb], R Core Team [ctb]

qtl_1.70.tar.gz
qtl_1.70.tar.gz(r-4.5-noble)qtl_1.70.tar.gz(r-4.4-noble)
qtl_1.70.tgz(r-4.4-emscripten)qtl_1.70.tgz(r-4.3-emscripten)
qtl.pdf |qtl.html
qtl/json (API)
NEWS

# Install 'qtl' in R:
install.packages('qtl', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kbroman/qtl/issues

Uses libs:
  • openblas– Optimized BLAS
Datasets:
  • badorder - An intercross with misplaced markers
  • bristle3 - Data on bristle number in Drosophila
  • bristleX - Data on bristle number in Drosophila
  • fake.4way - Simulated data for a 4-way cross
  • fake.bc - Simulated data for a backcross
  • fake.f2 - Simulated data for an F2 intercross
  • hyper - Data on hypertension
  • listeria - Data on Listeria monocytogenes susceptibility
  • locations - Genetic locations of traits for the multitrait dataset
  • map10 - An example genetic map
  • mapthis - Simulated data for illustrating genetic map construction
  • multitrait - Example Cross object from R/QTL with multiple traits

openblas

9.29 score 2 stars 28 packages 2.3k scripts 5.0k downloads 86 mentions 197 exports 0 dependencies

Last updated 4 months agofrom:d7403849e4. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linux-x86_64OKDec 01 2024

Exports:add.cim.covaradd.thresholdaddcovarintaddintaddloctocrossaddmarkeraddmarkerstointervalmapaddpairaddqtladdtoqtlallchrsplitsargmax.genobayesintcalc.errorlodcalc.genoprobcalc.penaltiescalc.plodcheckAllelescheckcovarcheckformulacheckStepwiseqtlStartchrlenchrnamescimcleancleanGenocomparecrossescomparegenocompareordercondenseconvertconvert2bcsftconvert2riselfconvert2risibconvert2sacountqtltermscountXOcreate.mapdeparseQTLformuladrop.dupmarkersdrop.markersdrop.nullmarkersdropfromqtldroponemarkereffectploteffectscanest.mapest.rffill.genofind_large_intervalsfind.flankingfind.markerfind.markerindexfind.markerposfind.phenofind.pseudomarkerfind.pseudomarkerposfindDupMarkersfitqtlfitqtlenginefitstahlflip.orderflipcrossformLinkageGroupsformMarkerCovargenAllPartitionsgeno.crosstabgeno.imagegeno.tablegetgenonamesgetidgetsexgroupclusteredheatmapimf.cfimf.himf.kimf.mimf.stahlinferFounderHapinferredpartitionsinterpPositionsjittermaplocatemarkerlocateXOlodintmakeqtlmap2tablemarkerlrtmarkernamesmatchchrmf.cfmf.hmf.kmf.mmf.stahlmovemarkermqm_versionmqmaugmentmqmautocofactorsmqmextractmarkersmqmfind.markermqmgetmodelmqmpermutationmqmplot.circlemqmplot.cistransmqmplot.clusteredheatmapmqmplot.cofactorsmqmplot.directedqtlmqmplot.heatmapmqmplot.multitraitmqmplot.permutationsmqmplot.singletraitmqmprocesspermutationmqmscanmqmscanallmqmscanfdrmqmsetcofactorsmqmtestnormalnchrnindnmarnmissingnphenqranknqtlntypednullmarkersorderMarkersparseformulaphenamespickMarkerSubsetplot.mapplotErrorlodplotGenoplotInfoplotLodProfileplotMapplotMissingplotModelplotPhenoplotPXGplotRFpolyplotpull.argmaxgenopull.drawspull.genopull.genoprobpull.mappull.markerspull.phenopull.rfqtlversionread.crossreadMWrilreduce2gridrefineqtlreorderqtlreplace.mapreplacemapreplaceqtlrescalemapreviseqtlnuminformulareviseXdataripplescanallscanonescanonebootscanonevarscanonevar.meanpermscanonevar.varpermscanPhyloQTLscanqtlscantwoscantwopermhkshiftmapsim.crosssim.genosim.mapsimFounderSnpssimPhyloQTLsimulatemissingdatastepwiseqtlstrip.partialssubrousummaryscantwosummary.mapsummaryMapsummaryScantwoOldswitch.orderswitchAllelestable2maptop.errorlodtotmartransformPhenotryallpositionstypingGapwrite.crossxaxisloc.scanone

Dependencies:

Users Guide for New BCsFt Tools for R/qtl

Rendered frombcsft.Rnwusingutils::Sweaveon Dec 01 2024.

Last update: 2021-01-07
Started: 2013-04-11

Readme and manuals

Help Manual

Help pageTopics
Introductory comments on R/qtlqtl-package
Indicate marker covariates from composite interval mappingadd.cim.covar
Add significance threshold to plotadd.threshold
Add QTL x covariate interaction to a multiple-QTL modeladdcovarint
Add pairwise interaction to a multiple-QTL modeladdint
Add phenotype location into a cross objectaddloctocross
Add a marker to a crossaddmarker
Scan for an additional pair of QTL in a multiple-QTL modeladdpair
Scan for an additional QTL in a multiple-QTL modeladdqtl
Add to a qtl objectaddtoqtl
Test all possible splits of a chromosome into two piecesallchrsplits
Reconstruct underlying genotypesargmax.geno
Arithmetic operators for scanone and scantwo results+.scanone +.scantwo -.scanone -.scantwo
Arithmetic Operators for permutation results+.scanoneperm +.scantwoperm -.scanoneperm -.scantwoperm
An intercross with misplaced markersbadorder
Bayesian credible intervalbayesint
Data on bristle number in Drosophilabristle3
Data on bristle number in DrosophilabristleX
Combine data for QTL experimentsc.cross
Combine columns from multiple scanone resultsc.scanone cbind.scanone
Combine data from scanone permutationsc.scanoneperm rbind.scanoneperm
Combine columns from multiple scantwo resultsc.scantwo cbind.scantwo
Combine data from scantwo permutationsc.scantwoperm rbind.scantwoperm
Identify likely genotyping errorscalc.errorlod
Calculate conditional genotype probabilitiescalc.genoprob
Calculate LOD penaltiescalc.penalties
Combine columns from multiple scanone permutation resultscbind.scanoneperm
Combine scantwo permutations by columncbind.scantwoperm
Identify markers with switched allelescheckAlleles
Chromosome lengths in QTL experimentchrlen
Pull out the chromosome names from a crosschrnames
Composite interval mappingcim
Remove derived dataclean.cross
Clean up scantwo outputclean.scantwo
Delete genotypes that are possibly in errorcleanGeno
Compare two cross objectscomparecrosses
Compare individuals' genotype datacomparegeno
Compare two orderings of markers on a chromosomecompareorder
Condense the output from a 2-d genome scancondense.scantwo
Change map function for a genetic mapconvert.map
Convert output from scanone for R/qtl version 0.98convert.scanone
Convert output from scantwo for R/qtl version 1.03 and earlierconvert.scantwo
Convert a cross to RIL by selfingconvert2riself
Convert a cross to RIL by sib matingconvert2risib
Convert a sex-specific map to a sex-averaged oneconvert2sa
Count number of obligate crossovers for each individualcountXO
Drop duplicate markersdrop.dupmarkers
Drop a set of markersdrop.markers
Drop markers without any genotype datadrop.nullmarkers
Drop a QTL from a qtl objectdropfromqtl
Drop one marker at a time and determine effect on genetic mapdroponemarker
Plot phenotype means against genotypes at one or two markerseffectplot
Plot estimated QTL effects across the whole genomeeffectscan
Estimate genetic mapsest.map
Estimate pairwise recombination fractionsest.rf
Simulated data for a 4-way crossfake.4way
Simulated data for a backcrossfake.bc
Simulated data for an F2 intercrossfake.f2
Fill holes in genotype datafill.geno
Find large intervals in a mapfind_large_intervals
Find flanking markers for a specified positionfind.flanking
Find marker closest to a specified positionfind.marker
Determine the numeric index for a markerfind.markerindex
Find position of a markerfind.markerpos
Find column number for a particular phenotypefind.pheno
Find the pseudomarker closest to a specified positionfind.pseudomarker
Find markers with identical genotype datafindDupMarkers
Fit a multiple-QTL modelfitqtl
Fit Stahl interference modelfitstahl
Flip the orders of markers on a set of chromosomesflip.order
Partition markers into linkage groupsformLinkageGroups
Create matrix of marker covariates for QTL analysisformMarkerCovar
Create table of two-locus genotypesgeno.crosstab
Plot grid of genotype datageno.image
Create table of genotype distributionsgeno.table
Pull out the individual identifiers from a crossgetid
Retrieving groups of traits after clusteringgroupclusteredheatmap
Data on hypertensionhyper
Crude reconstruction of founder haplotypes in multi-parent RILinferFounderHap
Identify inferred partitions in mapping QTL to a phylogenetic treeinferredpartitions
Interpolate positions from one map to anotherinterpPositions
Jitter marker positions in a genetic mapjittermap
Data on Listeria monocytogenes susceptibilitylisteria
Estimate locations of crossoverslocateXO
Genetic locations of traits for the multitrait datasetlocations
LOD support intervallodint
Make a qtl objectmakeqtl
An example genetic mapmap10
Convert genetic map from list to table.map2table
Simulated data for illustrating genetic map constructionmapthis
General likelihood ratio test for association between marker pairsmarkerlrt
Pull out the marker names from a crossmarkernames
Maximum peak in genome scanmax.scanone
Maximum peak in genome scan to map a QTL to a phylogenetic treemax.scanPhyloQTL
Maximum peak in two-dimensional genome scanmax.scantwo
Move a marker to a new chromosomemovemarker
Introduction to Multiple QTL Model (MQM) mappingMQM
MQM augmentationmqmaugment
Automatic setting of cofactors, taking marker density into accountmqmautocofactors
MQM marker extractionmqmextractmarkers
Fetch significant markers after permutation analysismqmfind.marker
Retrieve the QTL model used in mapping from the results of an MQM scanmqmgetmodel
Estimate QTL LOD score significance using permutations or simulationsmqmpermutation
Circular genome plot for MQMmqmplot.circle
cis-trans plotmqmplot.cistrans
Plot clustered heatmap of MQM scan on multiple phenotypesmqmplot.clusteredheatmap
Plot cofactors on the genetic mapmqmplot.cofactors
Plot LOD*Effect curves of a multiple-QTL modelmqmplot.directedqtl
Heatmap of a genome of MQM scan on multiple phenotypesmqmplot.heatmap
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypesmqmplot.multitrait
Plot results from mqmpermutationmqmplot.permutations
Plot LOD curves of a multiple-QTL modelmqmplot.singletrait
Convert mqmmulti objects into a scanoneperm objectmqmprocesspermutation
Genome scan with a multiple QTL model (MQM)mqmscan
Parallelized MQM on multiple phenotypes in a cross objectmqmscanall
Estimate FDR for multiple trait QTL analysismqmscanfdr
Set cofactors at fixed intervals, to be used with MQMmqmsetcofactors
Shapiro normality test used for MQMmqmtestnormal
Example Cross object from R/QTL with multiple traitsmultitrait
Determine the number of chromosomesnchr
Determine the number of individuals QTL experimentnind
Determine the numbers of markers on each chromosomenmar
Number of missing genotypesnmissing
Determine the number of phenotypes QTL experimentnphe
Transform a vector of quantitative values to the corresponding normal quantilesnqrank
Determine the number of QTL in a QTL objectnqtl
Number of genotypesntyped
Identify markers without any genotype datanullmarkers
Find an initial order for markers within chromosomesorderMarkers
Pull out the phenotypes names from a crossphenames
Identify the largest subset of markers that are some distance apartpickMarkerSubset
Plot genotype comparisonplot.comparegeno
Plot various features of a cross objectplot.cross
Plot QTL locationsplot.qtl
Plot recombination fractions or LOD scores for a single markerplot.rfmatrix
Plot LOD curvesplot.scanone
Plot results of bootstrap for QTL positionplot.scanoneboot
Plot permutation results for a single-QTL genome scanplot.scanoneperm
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic treeplot.scanPhyloQTL
Plot LOD scores for a two-dimensional genome scanplot.scantwo
Plot permutation results for a 2d, 2-QTL genome scanplot.scantwoperm
Plot grid of error LOD valuesplotErrorlod
Plot observed genotypes, flagging likely errorsplotGeno
Plot the proportion of missing genotype informationplotInfo
Plot 1-d LOD profiles for a multiple QTL modelplotLodProfile
Plot genetic mapplot.map plotMap
Plot grid of missing genotypesplotMissing
Plot a QTL modelplotModel
Plot a phenotype distributionplotPheno
Plot phenotypes versus marker genotypesplotPXG
Plot recombination fractionsplotRF
Pull out the results of the Viterbi algorithm from a crosspull.argmaxgeno
Pull out the genotype imputations from a crosspull.draws
Pull out the genotype data from a crosspull.geno
Pull out the genotype probabilities from a crosspull.genoprob
Pull out the genetic map from a crosspull.map
Drop all but a selected set of markerspull.markers
Pull out phenotype data from a crosspull.pheno
Pull out recombination fractions or LOD scores from a cross objectpull.rf
Installed version of R/qtlqtlversion
Read data for a QTL experimentread.cross
Read data for 4- or 8-way RILreadMWril
Reduce to a grid of pseudomarkers.reduce2grid
Refine the positions of QTLrefineqtl
Reorder the QTL in a qtl objectreorderqtl
Replace the genetic map of a crossreplace.map replacemap.cross
Replace the genetic map in QTL mapping results with an alternate mapreplacemap.scanone
Replace the genetic map in QTL mapping results with an alternate mapreplacemap.scantwo
Replace a QTL in a qtl object with a different positionreplaceqtl
Rescale genetic mapsrescalemap
Compare marker ordersripple
Genome scan with a single QTL modelscanone
Bootstrap to get interval estimate of QTL locationscanoneboot
Genome scan for QTL affecting mean and/or variancescanonevar
Permutation test for mean effect in scanonevarscanonevar.meanperm
Permutation test for variance effect in scanonevarscanonevar.varperm
Single-QTL genome scan to map QTL to a phylogenetic treescanPhyloQTL
General QTL scanscanqtl
Two-dimensional genome scan with a two-QTL modelscantwo
Permutation test for 2d genome scan by Haley-Knott regressionscantwopermhk
Shift starting points in genetic mapsshiftmap
Simulate a QTL experimentsim.cross
Simulate genotypes given observed marker datasim.geno
Simulate a genetic mapsim.map
Simulate founder SNPs for a multiple-strain RILsimFounderSnps
Simulate a set of intercrosses for a single diallelic QTLsimPhyloQTL
Simulates missing genotype datasimulatemissingdata
Stepwise selection for multiple QTLstepwiseqtl
Strip partially informative genotypesstrip.partials
Subsetting data for QTL experimentsubset.cross [.cross
Subsetting chromosomes for a genetic mapsubset.map [.map
Subsetting the results of a genome scansubset.scanone
Subsetting permutation test resultssubset.scanoneperm [.scanoneperm
Subsetting the results of a 2-d genome scansubset.scantwo
Subsetting two-dimensional permutation test resultssubset.scantwoperm [.scantwoperm
Print pairs of individuals with similar genotype data.summary.comparegeno
Print summary of QTL experimentsummary.cross
Summary of fit of qtl modelsummary.fitqtl
Print summary of a QTL objectsummary.qtl
Print summary of ripple resultssummary.ripple
Summarize the results of a genome scanssummary.scanone
Bootstrap confidence interval for QTL locationsummary.scanoneboot
LOD thresholds from scanone permutation resultssummary.scanoneperm
Summarize the results a genome scan to map a QTL to a phylogenetic treesummary.scanPhyloQTL
Summarize the results of a two-dimensional genome scansummary.scantwo
LOD thresholds from scantwo permutation resultssummary.scantwoperm
Print summary of a genetic mapsummary.map summaryMap
Summarize the results of a two-dimensional genome scansummaryScantwoOld
Switch the order of markers on a chromosomeswitch.order
Switch alleles at selected markersswitchAlleles
Convert a table of marker positions to a map object.table2map
List genotypes with large error LOD scorestop.errorlod
Determine the total number of markerstotmar
Transformation of the phenotypes in a cross objecttransformPheno
Test all possible positions for a markertryallpositions
Maximum distance between genotyped markerstypingGap
Write data for a QTL experiment to a filewrite.cross
Get x-axis locations in scanone plotxaxisloc.scanone