qtl: Tools for Analyzing QTL Experiments

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.

AuthorKarl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Date of publication2016-11-05 08:59:40
MaintainerKarl W Broman <kbroman@biostat.wisc.edu>
LicenseGPL-3
Version1.40-8
http://rqtl.org

View on CRAN

Man pages

add.cim.covar: Indicate marker covariates from composite interval mapping

addcovarint: Add QTL x covariate interaction to a multiple-QTL model

addint: Add pairwise interaction to a multiple-QTL model

addloctocross: Add phenotype location into a cross object

addmarker: Add a marker to a cross

addpair: Scan for an additional pair of QTL in a multiple-QTL model

addqtl: Scan for an additional QTL in a multiple-QTL model

add.threshold: Add significance threshold to plot

addtoqtl: Add to a qtl object

allchrsplits: Test all possible splits of a chromosome into two pieces

argmax.geno: Reconstruct underlying genotypes

arithscan: Arithmetic operators for scanone and scantwo results

arithscanperm: Arithmetic Operators for permutation results

a.starting.point: Introductory comments on R/qtl

badorder: An intercross with misplaced markers

bayesint: Bayesian credible interval

bristle3: Data on bristle number in Drosophila

bristleX: Data on bristle number in Drosophila

calc.errorlod: Identify likely genotyping errors

calc.genoprob: Calculate conditional genotype probabilities

calc.penalties: Calculate LOD penalties

cbind.scanoneperm: Combine columns from multiple scanone permutation results

cbind.scantwoperm: Combine scantwo permutations by column

c.cross: Combine data for QTL experiments

checkAlleles: Identify markers with switched alleles

chrlen: Chromosome lengths in QTL experiment

chrnames: Pull out the chromosome names from a cross

cim: Composite interval mapping

clean.cross: Remove derived data

cleanGeno: Delete genotypes that are possibly in error

clean.scantwo: Clean up scantwo output

comparecrosses: Compare two cross objects

comparegeno: Compare individuals' genotype data

compareorder: Compare two orderings of markers on a chromosome

condense.scantwo: Condense the output from a 2-d genome scan

convert2riself: Convert a cross to RIL by selfing

convert2risib: Convert a cross to RIL by sib mating

convert2sa: Convert a sex-specific map to a sex-averaged one

convert.map: Change map function for a genetic map

convert.scanone: Convert output from scanone for R/qtl version 0.98

convert.scantwo: Convert output from scantwo for R/qtl version 1.03 and...

countXO: Count number of obligate crossovers for each individual

c.scanone: Combine columns from multiple scanone results

c.scanoneperm: Combine data from scanone permutations

c.scantwo: Combine columns from multiple scantwo results

c.scantwoperm: Combine data from scantwo permutations

drop.dupmarkers: Drop duplicate markers

dropfromqtl: Drop a QTL from a qtl object

drop.markers: Drop a set of markers

drop.nullmarkers: Drop markers without any genotype data

droponemarker: Drop one marker at a time and determine effect on genetic map

effectplot: Plot phenotype means against genotypes at one or two markers

effectscan: Plot estimated QTL effects across the whole genome

est.map: Estimate genetic maps

est.rf: Estimate pairwise recombination fractions

fake.4way: Simulated data for a 4-way cross

fake.bc: Simulated data for a backcross

fake.f2: Simulated data for an F2 intercross

fill.geno: Fill holes in genotype data

findDupMarkers: Find markers with identical genotype data

find.flanking: Find flanking markers for a specified position

find.marker: Find marker closest to a specified position

findmarkerindex: Determine the numeric index for a marker

find.markerpos: Find position of a marker

find.pheno: Find column number for a particular phenotype

find.pseudomarker: Find the pseudomarker closest to a specified position

fitqtl: Fit a multiple-QTL model

fitstahl: Fit Stahl interference model

flip.order: Flip the orders of markers on a set of chromosomes

formLinkageGroups: Partition markers into linkage groups

formMarkerCovar: Create matrix of marker covariates for QTL analysis

geno.crosstab: Create table of two-locus genotypes

geno.image: Plot grid of genotype data

geno.table: Create table of genotype distributions

getid: Pull out the individual identifiers from a cross

groupclusteredheatmap: Retrieving groups of traits after clustering

hyper: Data on hypertension

inferFounderHap: Crude reconstruction of founder haplotypes in multi-parent...

inferredpartitions: Identify inferred partitions in mapping QTL to a phylogenetic...

interpPositions: Interpolate positions from one map to another

jittermap: Jitter marker positions in a genetic map

listeria: Data on Listeria monocytogenes susceptibility

locateXO: Estimate locations of crossovers

locations: Genetic locations of traits for the multitrait dataset

lodint: LOD support interval

makeqtl: Make a qtl object

map10: An example genetic map

map2table: Convert genetic map from list to table.

mapthis: Simulated data for illustrating genetic map construction

markerlrt: General likelihood ratio test for association between marker...

markernames: Pull out the marker names from a cross

max.scanone: Maximum peak in genome scan

max.scanPhyloQTL: Maximum peak in genome scan to map a QTL to a phylogenetic...

max.scantwo: Maximum peak in two-dimensional genome scan

movemarker: Move a marker to a new chromosome

MQM: Introduction to Multiple QTL Model (MQM) mapping

mqmaugment: MQM augmentation

mqmautocofactors: Automatic setting of cofactors, taking marker density into...

mqmextractmarkers: MQM marker extraction

mqmfind.marker: Fetch significant markers after permutation analysis

mqmgetmodel: Retrieve the QTL model used in mapping from the results of an...

mqmpermutation: Estimate QTL LOD score significance using permutations or...

mqmplotcircle: Circular genome plot for MQM

mqmplotcistrans: cis-trans plot

mqmplotclusteredheatmap: Plot clustered heatmap of MQM scan on multiple phenotypes

mqmplotcofactors: Plot cofactors on the genetic map

mqmplotdirectedqtl: Plot LOD*Effect curves of a multiple-QTL model

mqmplotheatmap: Heatmap of a genome of MQM scan on multiple phenotypes

mqmplotmultitrait: Plot the results from a genomescan using a multiple-QTL model...

mqmplotpermutations: Plot results from mqmpermutation

mqmplotsingletrait: Plot LOD curves of a multiple-QTL model

mqmprocesspermutation: Convert mqmmulti objects into a scanoneperm object

mqmscan: Genome scan with a multiple QTL model (MQM)

mqmscanall: Parallelized MQM on multiple phenotypes in a cross object

mqmscanfdr: Estimate FDR for multiple trait QTL analysis

mqmsetcofactors: Set cofactors at fixed intervals, to be used with MQM

mqmtestnormal: Shapiro normality test used for MQM

multitrait: Example Cross object from R/QTL with multiple traits

nchr: Determine the number of chromosomes

nind: Determine the number of individuals QTL experiment

nmar: Determine the numbers of markers on each chromosome

nmissing: Number of missing genotypes

nphe: Determine the number of phenotypes QTL experiment

nqrank: Transform a vector of quantitative values to the...

nqtl: Determine the number of QTL in a QTL object

ntyped: Number of genotypes

nullmarkers: Identify markers without any genotype data

orderMarkers: Find an initial order for markers within chromosomes

phenames: Pull out the phenotypes names from a cross

pickMarkerSubset: Identify the largest subset of markers that are some distance...

plot.cross: Plot various features of a cross object

plot.errorlod: Plot grid of error LOD values

plot.geno: Plot observed genotypes, flagging likely errors

plot.info: Plot the proportion of missing genotype information

plotLodProfile: Plot 1-d LOD profiles for a multiple QTL model

plot.map: Plot genetic map

plot.missing: Plot grid of missing genotypes

plotModel: Plot a QTL model

plot.pheno: Plot a phenotype distribution

plot.pxg: Plot phenotypes versus marker genotypes

plot.qtl: Plot QTL locations

plot.rf: Plot recombination fractions

plot.rfmatrix: Plot recombination fractions or LOD scores for a single...

plot.scanone: Plot LOD curves

plot.scanoneboot: Plot results of bootstrap for QTL position

plot.scanoneperm: Plot permutation results for a single-QTL genome scan

plot.scanPhyloQTL: Plot LOD curves from single-QTL scan to map QTL to a...

plot.scantwo: Plot LOD scores for a two-dimensional genome scan

plot.scantwoperm: Plot permutation results for a 2d, 2-QTL genome scan

pull.argmaxgeno: Pull out the results of the Viterbi algorithm from a cross

pull.draws: Pull out the genotype imputations from a cross

pull.geno: Pull out the genotype data from a cross

pull.genoprob: Pull out the genotype probabilities from a cross

pull.map: Pull out the genetic map from a cross

pull.markers: Drop all but a selected set of markers

pull.pheno: Pull out phenotype data from a cross

pull.rf: Pull out recombination fractions or LOD scores from a cross...

qtl-internal: Internal qtl functions

qtlversion: Installed version of R/qtl

read.cross: Read data for a QTL experiment

readMWril: Read data for 4- or 8-way RIL

reduce2grid: Reduce to a grid of pseudomarkers.

refineqtl: Refine the positions of QTL

reorderqtl: Reorder the QTL in a qtl object

replace.map: Replace the genetic map of a cross

replacemap.scanone: Replace the genetic map in QTL mapping results with an...

replacemap.scantwo: Replace the genetic map in QTL mapping results with an...

replaceqtl: Replace a QTL in a qtl object with a different position

rescalemap: Rescale genetic maps

ripple: Compare marker orders

scanone: Genome scan with a single QTL model

scanoneboot: Bootstrap to get interval estimate of QTL location

scanonevar: Genome scan for QTL affecting mean and/or variance

scanonevar.meanperm: Permutation test for mean effect in scanonevar

scanonevar.varperm: Permutation test for variance effect in scanonevar

scanPhyloQTL: Single-QTL genome scan to map QTL to a phylogenetic tree

scanqtl: General QTL scan

scantwo: Two-dimensional genome scan with a two-QTL model

scantwopermhk: Permutation test for 2d genome scan by Haley-Knott regression

shiftmap: Shift starting points in genetic maps

sim.cross: Simulate a QTL experiment

simFounderSnps: Simulate founder SNPs for a multiple-strain RIL

sim.geno: Simulate genotypes given observed marker data

sim.map: Simulate a genetic map

simPhyloQTL: Simulate a set of intercrosses for a single diallelic QTL

simulateMissingData: Simulates missing genotype data

stepwiseqtl: Stepwise selection for multiple QTL

strip.partials: Strip partially informative genotypes

subset.cross: Subsetting data for QTL experiment

subset.map: Subsetting chromosomes for a genetic map

subset.scanone: Subsetting the results of a genome scan

subset.scanoneperm: Subsetting permutation test results

subset.scantwo: Subsetting the results of a 2-d genome scan

subset.scantwoperm: Subsetting two-dimensional permutation test results

summary.cross: Print summary of QTL experiment

summary.fitqtl: Summary of fit of qtl model

summary.map: Print summary of a genetic map

summary.qtl: Print summary of a QTL object

summary.ripple: Print summary of ripple results

summary.scanone: Summarize the results of a genome scans

summary.scanoneboot: Bootstrap confidence interval for QTL location

summary.scanoneperm: LOD thresholds from scanone permutation results

summary.scanPhyloQTL: Summarize the results a genome scan to map a QTL to a...

summary.scantwo: Summarize the results of a two-dimensional genome scan

summary.scantwo.old: Summarize the results of a two-dimensional genome scan

summary.scantwoperm: LOD thresholds from scantwo permutation results

switchAlleles: Switch alleles at selected markers

switch.order: Switch the order of markers on a chromosome

table2map: Convert a table of marker positions to a map object.

top.errorlod: List genotypes with large error LOD scores

totmar: Determine the total number of markers

transformPheno: Transformation of the phenotypes in a cross object

tryallpositions: Test all possible positions for a marker

typingGap: Maximum distance between genotyped markers

write.cross: Write data for a QTL experiment to a file

xaxisloc.scanone: Get x-axis locations in scanone plot

Functions

add.cim.covar Man page
addcovarint Man page
addint Man page
addloctocross Man page
addmarker Man page
addmarkerstointervalmap Man page
addpair Man page
addqtl Man page
add.threshold Man page
addtoqtl Man page
allchrsplits Man page
argmax.geno Man page
badorder Man page
bayesint Man page
bristle3 Man page
bristleX Man page
calc.errorlod Man page
calc.genoprob Man page
calc.penalties Man page
calc.plod Man page
cbind.scanone Man page
cbind.scanoneperm Man page
cbind.scantwo Man page
cbind.scantwoperm Man page
c.cross Man page
checkAlleles Man page
checkcovar Man page
checkformula Man page
checkStepwiseqtlStart Man page
chrlen Man page
chrnames Man page
cim Man page
clean Man page
clean.cross Man page
cleanGeno Man page
clean.scantwo Man page
comparecrosses Man page
comparegeno Man page
compareorder Man page
condense Man page
condense.scantwo Man page
convert Man page
convert2bcsft Man page
convert2riself Man page
convert2risib Man page
convert2sa Man page
convert.map Man page
convert.scanone Man page
convert.scantwo Man page
countqtlterms Man page
countXO Man page
create.map Man page
[.cross Man page
c.scanone Man page
c.scanoneperm Man page
c.scantwo Man page
c.scantwoperm Man page
deparseQTLformula Man page
drop.dupmarkers Man page
dropfromqtl Man page
drop.markers Man page
drop.nullmarkers Man page
droponemarker Man page
effectplot Man page
effectscan Man page
est.map Man page
est.rf Man page
fake.4way Man page
fake.bc Man page
fake.f2 Man page
fill.geno Man page
findDupMarkers Man page
find.flanking Man page
find.marker Man page
find.markerindex Man page
find.markerpos Man page
find.pheno Man page
find.pseudomarker Man page
find.pseudomarkerpos Man page
fitqtl Man page
fitqtlengine Man page
fitstahl Man page
flipcross Man page
flip.order Man page
formLinkageGroups Man page
formMarkerCovar Man page
genAllPartitions Man page
geno.crosstab Man page
geno.image Man page
geno.table Man page
getgenonames Man page
getid Man page
getsex Man page
groupclusteredheatmap Man page
hyper Man page
imf.cf Man page
imf.h Man page
imf.k Man page
imf.m Man page
imf.stahl Man page
inferFounderHap Man page
inferredpartitions Man page
interpPositions Man page
jittermap Man page
listeria Man page
locatemarker Man page
locateXO Man page
locations Man page
lodint Man page
makeqtl Man page
[.map Man page
map10 Man page
map2table Man page
mapthis Man page
markerlrt Man page
markernames Man page
matchchr Man page
max.scanone Man page
max.scanPhyloQTL Man page
max.scantwo Man page
max.scantwocondensed Man page
mf.cf Man page
mf.h Man page
mf.k Man page
mf.m Man page
mf.stahl Man page
movemarker Man page
MQM Man page
mqmaugment Man page
mqmautocofactors Man page
mqmextractmarkers Man page
mqmfind.marker Man page
mqmgetmodel Man page
mqmgetmodel Man page
mqmpermutation Man page
mqmplot.circle Man page
mqmplot.cistrans Man page
mqmplot.clusteredheatmap Man page
mqmplot.cofactors Man page
mqmplot.directedqtl Man page
mqmplot.heatmap Man page
mqmplot.multitrait Man page
mqmplot.permutations Man page
mqmplot.singletrait Man page
mqmprocesspermutation Man page
mqmscan Man page
mqmscanall Man page
mqmscanfdr Man page
mqmsetcofactors Man page
mqmtestnormal Man page
mqm_version Man page
multitrait Man page
nchr Man page
nind Man page
nmar Man page
nmissing Man page
nphe Man page
nqrank Man page
nqtl Man page
ntyped Man page
nullmarkers Man page
orderMarkers Man page
parseformula Man page
phenames Man page
pickMarkerSubset Man page
plot.cross Man page
plot.errorlod Man page
plotErrorlod Man page
plot.geno Man page
plotGeno Man page
plot.info Man page
plotInfo Man page
plotLodProfile Man page
plot.map Man page
plotMap Man page
plot.missing Man page
plotMissing Man page
plotModel Man page
plot.pheno Man page
plotPheno Man page
plot.pxg Man page
plotPXG Man page
plot.qtl Man page
plot.rf Man page
plotRF Man page
plot.rfmatrix Man page
plot.scanone Man page
plot.scanoneboot Man page
plot.scanoneperm Man page
plot.scanPhyloQTL Man page
plot.scantwo Man page
plot.scantwoperm Man page
polyplot Man page
print.addcovarint Man page
print.addint Man page
print.compactqtl Man page
print.cross Man page
print.map Man page
print.qtl Man page
print.scanoneboot Man page
print.scantwo Man page
print.summary.addpair Man page
print.summary.compactqtl Man page
print.summary.cross Man page
print.summary.fitqtl Man page
print.summary.map Man page
print.summary.qtl Man page
print.summary.ripple Man page
print.summary.scanone Man page
print.summary.scanoneperm Man page
print.summary.scantwo Man page
print.summary.scantwo.old Man page
print.summary.scantwoperm Man page
pull.argmaxgeno Man page
pull.draws Man page
pull.geno Man page
pull.genoprob Man page
pull.map Man page
pull.markers Man page
pull.pheno Man page
pull.rf Man page
qtl-package Man page
qtlversion Man page
rbind.scanoneperm Man page
rbind.scantwoperm Man page
read.cross Man page
readMWril Man page
reduce2grid Man page
refineqtl Man page
reorderqtl Man page
replacemap Man page
replace.map Man page
replacemap.cross Man page
replacemap.scanone Man page
replacemap.scantwo Man page
replaceqtl Man page
rescalemap Man page
reviseqtlnuminformula Man page
reviseXdata Man page
ripple Man page
scanall Man page
scanone Man page
-.scanone Man page
+.scanone Man page
scanoneboot Man page
-.scanoneperm Man page
[.scanoneperm Man page
+.scanoneperm Man page
scanonevar Man page
scanonevar.meanperm Man page
scanonevar.varperm Man page
scanPhyloQTL Man page
scanqtl Man page
scantwo Man page
-.scantwo Man page
+.scantwo Man page
-.scantwoperm Man page
[.scantwoperm Man page
+.scantwoperm Man page
scantwopermhk Man page
shiftmap Man page
sim.cross Man page
simFounderSnps Man page
sim.geno Man page
sim.map Man page
simPhyloQTL Man page
simulatemissingdata Man page
stepwiseqtl Man page
strip.partials Man page
subrousummaryscantwo Man page
subset.cross Man page
subset.map Man page
subset.scanone Man page
subset.scanoneperm Man page
subset.scantwo Man page
subset.scantwoperm Man page
summary.addcovarint Man page
summary.addint Man page
summary.compactqtl Man page
summary.cross Man page
summary.fitqtl Man page
summary.map Man page
summaryMap Man page
summary.qtl Man page
summary.ripple Man page
summary.scanone Man page
summary.scanoneboot Man page
summary.scanoneperm Man page
summary.scanPhyloQTL Man page
summary.scantwo Man page
summary.scantwocondensed Man page
summaryScantwoOld Man page
summary.scantwoperm Man page
switchAlleles Man page
switch.order Man page
table2map Man page
top.errorlod Man page
totmar Man page
transformPheno Man page
tryallpositions Man page
typingGap Man page
write.cross Man page
xaxisloc.scanone Man page

Files

qtl
qtl/inst
qtl/inst/BUGS.txt
qtl/inst/CITATION
qtl/inst/TODO.txt
qtl/inst/STATUS.txt
qtl/inst/LICENSE.txt
qtl/inst/MQM-TODO.txt
qtl/inst/README.md
qtl/inst/INSTALL_ME.txt
qtl/inst/doc
qtl/inst/doc/geneticmaps.pdf
qtl/inst/doc/Sources
qtl/inst/doc/Sources/new_multiqtl.Rnw
qtl/inst/doc/Sources/rqtltour.tex
qtl/inst/doc/Sources/rqtltour2.tex
qtl/inst/doc/Sources/new_summary_scantwo.Rnw
qtl/inst/doc/Sources/geneticmaps.Rnw
qtl/inst/doc/Sources/new_summary_scanone.Rnw
qtl/inst/doc/Sources/MQM
qtl/inst/doc/Sources/MQM/sweaveit.sh
qtl/inst/doc/Sources/MQM/MQM-tour.Rnw
qtl/inst/doc/Sources/MQM/mqm
qtl/inst/doc/Sources/MQM/mqm/description.txt
qtl/inst/doc/Sources/MQM/mqm/standard_references.txt
qtl/inst/doc/Sources/MQM/mqm/standard_example.txt
qtl/inst/doc/Sources/MQM/mqm/standard_seealso.txt
qtl/inst/doc/Sources/MQM/mqm/limitations.txt
qtl/inst/doc/Sources/MQM/mqm/advantages_latex.txt
qtl/inst/doc/Sources/MQM/mqm/advantages_Rd.txt
qtl/inst/doc/Sources/MQM/mqm/significance_references.txt
qtl/inst/doc/Sources/MQM/mqm/parallelisation_references.txt
qtl/inst/doc/Sources/MQM/SweaveIt.R
qtl/inst/doc/Sources/MQM/sweaveit.bat
qtl/inst/doc/bcsft.pdf
qtl/inst/doc/new_multiqtl.R
qtl/inst/doc/rqtltour2.pdf
qtl/inst/doc/rqtltour2.R
qtl/inst/doc/bcsft.Rnw
qtl/inst/doc/new_summary_scantwo.pdf
qtl/inst/doc/geneticmaps.R
qtl/inst/doc/new_multiqtl.pdf
qtl/inst/doc/bcsft.R
qtl/inst/doc/new_summary_scanone.R
qtl/inst/doc/rqtltour.R
qtl/inst/doc/rqtltour.pdf
qtl/inst/doc/new_summary_scantwo.R
qtl/inst/doc/new_summary_scanone.pdf
qtl/inst/contrib
qtl/inst/contrib/biolib
qtl/inst/contrib/biolib/CMakeLists.txt
qtl/inst/contrib/biolib/README
qtl/inst/contrib/scripts
qtl/inst/contrib/scripts/check_rqtl.sh
qtl/inst/contrib/scripts/cleanup.sh
qtl/inst/contrib/scripts/repl_inputs.rb
qtl/inst/contrib/scripts/run_all_tests.sh
qtl/inst/contrib/scripts/update_header.rb
qtl/inst/contrib/scripts/install_rqtl.sh
qtl/inst/contrib/bin
qtl/inst/contrib/bin/mqmdebugout.cpp
qtl/inst/contrib/bin/CMakeLists.txt
qtl/inst/contrib/bin/wincompile.bat
qtl/inst/contrib/bin/scripts
qtl/inst/contrib/bin/scripts/cleanup.sh
qtl/inst/contrib/bin/scripts/profiler.sh
qtl/inst/contrib/bin/scripts/r.sh
qtl/inst/contrib/bin/scripts/regression_tests.sh
qtl/inst/contrib/bin/scripts/create-diff.sh
qtl/inst/contrib/bin/scripts/regression_tests_windows.bat
qtl/inst/contrib/bin/mqmmain.cpp
qtl/inst/contrib/bin/README
qtl/inst/contrib/bin/FindRLibs.cmake
qtl/inst/contrib/bin/regressiontests.bat
qtl/inst/contrib/bin/test
qtl/inst/contrib/bin/test/chridhyper.txt
qtl/inst/contrib/bin/test/filledgenohyper.txt
qtl/inst/contrib/bin/test/t12
qtl/inst/contrib/bin/test/t12/cofactors.txt
qtl/inst/contrib/bin/test/settingshyper.txt
qtl/inst/contrib/bin/test/phenohyper.txt
qtl/inst/contrib/bin/test/pheno.dat
qtl/inst/contrib/bin/test/genohyper.txt
qtl/inst/contrib/bin/test/t11
qtl/inst/contrib/bin/test/t11/cofactors.txt
qtl/inst/contrib/bin/test/regression
qtl/inst/contrib/bin/test/regression/t25out.txt
qtl/inst/contrib/bin/test/regression/t24out.txt
qtl/inst/contrib/bin/test/regression/t33out.txt
qtl/inst/contrib/bin/test/regression/t11out-test0.txt
qtl/inst/contrib/bin/test/regression/t32out.txt
qtl/inst/contrib/bin/test/regression/debugout_pbeta.txt
qtl/inst/contrib/bin/test/regression/debugout_dnorm.txt
qtl/inst/contrib/bin/test/regression/t34out.txt
qtl/inst/contrib/bin/test/regression/t12out.txt
qtl/inst/contrib/bin/test/regression/t31out.txt
qtl/inst/contrib/bin/test/regression/t21out.txt
qtl/inst/contrib/bin/test/regression/t13out.txt
qtl/inst/contrib/bin/test/regression/t23out.txt
qtl/inst/contrib/bin/test/regression/t22out.txt
qtl/inst/contrib/bin/test/regression/t11out.txt
qtl/inst/contrib/bin/test/cofactors.txt
qtl/inst/contrib/bin/test/std
qtl/inst/contrib/bin/test/std/settings3.txt
qtl/inst/contrib/bin/test/std/phenotypes2.txt
qtl/inst/contrib/bin/test/std/settings2.txt
qtl/inst/contrib/bin/test/std/genotypes3.txt
qtl/inst/contrib/bin/test/std/genotypes2.txt
qtl/inst/contrib/bin/test/std/genotypes1.txt
qtl/inst/contrib/bin/test/std/phenotypes3.txt
qtl/inst/contrib/bin/test/std/genotypes2m.txt
qtl/inst/contrib/bin/test/std/markers1.txt
qtl/inst/contrib/bin/test/std/settings1.txt
qtl/inst/contrib/bin/test/std/markers2.txt
qtl/inst/contrib/bin/test/std/genotypes3m.txt
qtl/inst/contrib/bin/test/std/markers3.txt
qtl/inst/contrib/bin/test/std/phenotypes1.txt
qtl/inst/contrib/bin/test/t33
qtl/inst/contrib/bin/test/t33/cofactors.txt
qtl/inst/contrib/bin/test/settings.dat
qtl/inst/contrib/bin/test/geno.dat
qtl/inst/contrib/bin/test/chrid.dat
qtl/inst/contrib/bin/test/t23
qtl/inst/contrib/bin/test/t23/cofactors.txt
qtl/inst/contrib/bin/test/markerpos.txt
qtl/inst/contrib/bin/test/t22
qtl/inst/contrib/bin/test/t22/cofactors.txt
qtl/inst/contrib/bin/test/markerposhyper.txt
qtl/inst/contrib/bin/rtest
qtl/inst/contrib/bin/rtest/test_mqm_hyper_prob.R
qtl/inst/contrib/bin/rtest/regression
qtl/inst/contrib/bin/rtest/regression/scanone_mr.rtest
qtl/inst/contrib/bin/rtest/regression/mqm_listeria1.rtest
qtl/inst/contrib/bin/rtest/test_mqm_listeria1.R
qtl/inst/contrib/bin/rtest/test_augmentation.R
qtl/inst/contrib/bin/rtest/test_scanone_mr.R
qtl/inst/sampledata
qtl/inst/sampledata/listeria_qc_cro.txt
qtl/inst/sampledata/listeria_qc_map.txt
qtl/inst/sampledata/listeria.csv
qtl/inst/sampledata/gen.txt
qtl/inst/sampledata/listeria_gen_rot.csv
qtl/inst/sampledata/listeria_phe_rot.csv
qtl/inst/sampledata/listeria_gen.csv
qtl/inst/sampledata/listeria_rot.csv
qtl/inst/sampledata/listeria.qtx
qtl/inst/sampledata/phe.txt
qtl/inst/sampledata/listeria_phe.csv
qtl/inst/sampledata/listeria_maps.txt
qtl/inst/sampledata/map.txt
qtl/inst/sampledata/README.txt
qtl/inst/sampledata/listeria_raw.txt
qtl/inst/sampledata/listeria_map.txt
qtl/tests
qtl/tests/listeria.csv
qtl/tests/gen.txt
qtl/tests/listeria.map
qtl/tests/test_scanonevar.R
qtl/tests/test_io.R
qtl/tests/testaugmentation.R
qtl/tests/test_tidyIO.Rout.save
qtl/tests/test_io.Rout.save
qtl/tests/phe.txt
qtl/tests/listeria2.map
qtl/tests/test_qtl.R
qtl/tests/test_mapqtl_io.R
qtl/tests/map.txt
qtl/tests/test_mapqtl_io.Rout.save
qtl/tests/testthat.R
qtl/tests/listeria2.csv
qtl/tests/testthat
qtl/tests/testthat/test-scantwoperm.R
qtl/tests/testthat/test-fliporder.R
qtl/tests/testthat/test-stepwiseqtl.R
qtl/tests/listeria.raw
qtl/tests/test_tidyIO.R
qtl/tests/test_scanonevar.Rout.save
qtl/src
qtl/src/hmm_main.h
qtl/src/mqmprob.cpp
qtl/src/mqmmixture.cpp
qtl/src/hmm_bcsft.h
qtl/src/fitqtl_imp_binary.h
qtl/src/fitqtl_imp_binary.c
qtl/src/Makevars
qtl/src/util.c
qtl/src/scanone_em.h
qtl/src/markerlrt.h
qtl/src/scantwo_binary_em.h
qtl/src/mqmdatatypes.cpp
qtl/src/mqmmapqtl.cpp
qtl/src/scantwo_imp.c
qtl/src/fitqtl_imp.c
qtl/src/hmm_ri4sib.h
qtl/src/simulate.c
qtl/src/hmm_util.c
qtl/src/hmm_bci.c
qtl/src/stahl_mf.c
qtl/src/inferFounderHap.h
qtl/src/scantwo_em.h
qtl/src/hmm_bgmagic16.c
qtl/src/hmm_ri8self.h
qtl/src/mqmeliminate.h
qtl/src/effectscan.c
qtl/src/scanone_mr.h
qtl/src/mqmeliminate.cpp
qtl/src/fitqtl_hk_binary.c
qtl/src/hmm_f2i.c
qtl/src/scanone_imp.c
qtl/src/ril48_reorg.h
qtl/src/hmm_ri8sib.c
qtl/src/vbscan.h
qtl/src/fill_geno_nodblXO.h
qtl/src/mqmregression.cpp
qtl/src/scanone_hk_binary.h
qtl/src/hmm_ri8sib.h
qtl/src/scantwopermhk.c
qtl/src/scanone_em_covar.h
qtl/src/hmm_f2i.h
qtl/src/discan_covar.h
qtl/src/hmm_bci.h
qtl/src/ripple.c
qtl/src/forwsel.h
qtl/src/simulate_ril.c
qtl/src/scanone_ehk.c
qtl/src/hmm_ri8selfIRIP1.h
qtl/src/mqmscan.h
qtl/src/mqmregression.h
qtl/src/scantwo_mr.c
qtl/src/standalone.h
qtl/src/test_bcsft.c
qtl/src/countXO.c
qtl/src/mqm.h
qtl/src/hmm_bcsft.c
qtl/src/mqmmapqtl.h
qtl/src/hmm_bc.c
qtl/src/hmm_util.h
qtl/src/scantwo_binary_hk.h
qtl/src/scanone_np.c
qtl/src/info.c
qtl/src/scanone_ehk.h
qtl/src/lapackutil.h
qtl/src/scanone_em.c
qtl/src/vbscan.c
qtl/src/simulate.h
qtl/src/scantwo_binary_em.c
qtl/src/util.h
qtl/src/summary_scantwo.h
qtl/src/scanone_mr.c
qtl/src/findDupMarkers_notexact.h
qtl/src/mqmprob.h
qtl/src/hmm_f2.c
qtl/src/mqmaugment.h
qtl/src/scantwopermhk.h
qtl/src/fitqtl_hk_binary.h
qtl/src/inferFounderHap.c
qtl/src/hmm_4way.h
qtl/src/hmm_ri8selfIRIP1.c
qtl/src/fitqtl_hk.h
qtl/src/scanone_hk.h
qtl/src/scantwo_em.c
qtl/src/hmm_bgmagic16.h
qtl/src/scanone_hk_binary.c
qtl/src/mqmmixture.h
qtl/src/scantwo_hk.c
qtl/src/scantwo_binary_hk.c
qtl/src/hmm_ri8self.c
qtl/src/fitqtl_imp.h
qtl/src/hmm_ri4sib.c
qtl/src/zeroin.c
qtl/src/mqmscan.cpp
qtl/src/scantwo_mr.h
qtl/src/lapackutil.c
qtl/src/hmm_ri4self.c
qtl/src/scantwo_imp.h
qtl/src/fitqtl_hk.c
qtl/src/ripple.h
qtl/src/scanone_hk.c
qtl/src/pickMarkerSubset.h
qtl/src/hmm_4way.c
qtl/src/zeroin.h
qtl/src/fill_geno_nodblXO.c
qtl/src/markerlrt.c
qtl/src/scantwo_hk.h
qtl/src/pickMarkerSubset.c
qtl/src/effectscan.h
qtl/src/discan.h
qtl/src/hmm_ri4self.h
qtl/src/scanone_em_covar.c
qtl/src/discan_covar.c
qtl/src/mqmdatatypes.h
qtl/src/summary_scantwo.c
qtl/src/findDupMarkers_notexact.c
qtl/src/countXO.h
qtl/src/scanone_np.h
qtl/src/scanone_imp.h
qtl/src/ril48_reorg.c
qtl/src/info.h
qtl/src/hmm_main.c
qtl/src/discan.c
qtl/src/simulate_ril.h
qtl/src/hmm_f2.h
qtl/src/forwsel.c
qtl/src/mqmaugment.cpp
qtl/src/stahl_mf.h
qtl/src/hmm_bc.h
qtl/NAMESPACE
qtl/data
qtl/data/bristleX.RData
qtl/data/fake.f2.RData
qtl/data/listeria.RData
qtl/data/map10.RData
qtl/data/hyper.RData
qtl/data/locations.RData
qtl/data/multitrait.RData
qtl/data/fake.4way.RData
qtl/data/fake.bc.RData
qtl/data/badorder.RData
qtl/data/bristle3.RData
qtl/data/mapthis.RData
qtl/R
qtl/R/read.cross.gary.R qtl/R/refineqtl.R qtl/R/scantwo.R qtl/R/sim.geno.R qtl/R/est.map.R qtl/R/mqmaugment.R qtl/R/plotperm.R qtl/R/markerlrt.R qtl/R/cim.R qtl/R/inferFounderHap.R qtl/R/map_construction.R qtl/R/plot.scanone.R qtl/R/scanone.R qtl/R/scanonevar.varperm.R qtl/R/stepwiseqtlX.R qtl/R/read.cross.R qtl/R/transformPheno.R qtl/R/effectscan.R qtl/R/addmarker.R qtl/R/plot.R qtl/R/fitstahl.R qtl/R/ripple.R qtl/R/plot.scantwo.R qtl/R/scantwopermhk.R qtl/R/plotModel.R qtl/R/readMWril.R qtl/R/vbscan.R qtl/R/scanonevar.meanperm.R qtl/R/add_threshold.R qtl/R/write.cross.mq.R qtl/R/errorlod.R qtl/R/summary.scantwo.old.R qtl/R/mqmcircleplot.R qtl/R/read.cross.csvs.R qtl/R/summary.cross.R qtl/R/mqmsnow.R qtl/R/pickMarkerSubset.R qtl/R/calc.pairprob.R qtl/R/mqmplots.R qtl/R/argmax.geno.R qtl/R/arithscan.R qtl/R/addqtl.R qtl/R/est.rf.R qtl/R/summary.scanone.R qtl/R/mqmscanall.R qtl/R/write.cross.qtab.R qtl/R/write.cross.R qtl/R/scanqtl.R qtl/R/effectplot.R qtl/R/xchr.R qtl/R/pull_stuff.R qtl/R/read.cross.csv.R qtl/R/mqmpermutation.R qtl/R/viridis.R qtl/R/tryallpositions.R qtl/R/read.cross.karl.R qtl/R/phyloqtl_util.R qtl/R/summary.scantwo.R qtl/R/replacemap.R qtl/R/mqmscan.R qtl/R/bcsft.R qtl/R/droponemarker.R qtl/R/phyloqtl_sim.R qtl/R/mqmutil.R qtl/R/discan.R qtl/R/fitqtl.R qtl/R/simulate.R qtl/R/mqmprepare.R qtl/R/read.cross.mm.R qtl/R/calc.genoprob.R qtl/R/add.cim.covar.R qtl/R/util.R qtl/R/read.cross.mq.R qtl/R/stepwiseqtl.R qtl/R/makeqtl.R qtl/R/scanonevar.R qtl/R/scanoneboot.R qtl/R/countXO.R qtl/R/sim_ril.R qtl/R/mqmcofactors.R qtl/R/interpPositions.R qtl/R/read.cross.tidy.R qtl/R/compareorder.R qtl/R/read.cross.qtx.R qtl/R/qtlcart_io.R qtl/R/phyloqtl_scan.R qtl/R/ril48_reorg.R
qtl/vignettes
qtl/vignettes/fancyheadings.sty
qtl/vignettes/recombinationcount.pdf
qtl/vignettes/bcsft.Rnw
qtl/vignettes/genotypeprobabilities.pdf
qtl/vignettes/why_we_need_a_new_program.pdf
qtl/vignettes/goldensectionsearch.pdf
qtl/vignettes/plos.bst
qtl/vignettes/vignette.bib
qtl/MD5
qtl/build
qtl/build/vignette.rds
qtl/DESCRIPTION
qtl/man
qtl/man/mqmplotheatmap.Rd qtl/man/replacemap.scantwo.Rd qtl/man/orderMarkers.Rd qtl/man/add.threshold.Rd qtl/man/scanonevar.Rd qtl/man/mqmtestnormal.Rd qtl/man/nmar.Rd qtl/man/mqmplotpermutations.Rd qtl/man/plot.scantwoperm.Rd qtl/man/pull.geno.Rd qtl/man/geno.crosstab.Rd qtl/man/bristle3.Rd qtl/man/compareorder.Rd qtl/man/summary.scantwo.Rd qtl/man/summary.scantwo.old.Rd qtl/man/scanPhyloQTL.Rd qtl/man/condense.scantwo.Rd qtl/man/pull.pheno.Rd qtl/man/est.map.Rd qtl/man/getid.Rd qtl/man/drop.nullmarkers.Rd qtl/man/mqmplotdirectedqtl.Rd qtl/man/scantwo.Rd qtl/man/replaceqtl.Rd qtl/man/tryallpositions.Rd qtl/man/convert2sa.Rd qtl/man/scanonevar.meanperm.Rd qtl/man/addmarker.Rd qtl/man/cleanGeno.Rd qtl/man/summary.scanoneperm.Rd qtl/man/simPhyloQTL.Rd qtl/man/totmar.Rd qtl/man/multitrait.Rd qtl/man/nqtl.Rd qtl/man/markerlrt.Rd qtl/man/markernames.Rd qtl/man/plotModel.Rd qtl/man/mqmscan.Rd qtl/man/nphe.Rd qtl/man/makeqtl.Rd qtl/man/mqmgetmodel.Rd qtl/man/inferFounderHap.Rd qtl/man/pull.markers.Rd qtl/man/bristleX.Rd qtl/man/summary.qtl.Rd qtl/man/bayesint.Rd qtl/man/plot.scantwo.Rd qtl/man/subset.scantwo.Rd qtl/man/summary.scanoneboot.Rd qtl/man/nind.Rd qtl/man/plot.errorlod.Rd qtl/man/mqmplotclusteredheatmap.Rd qtl/man/plot.qtl.Rd qtl/man/max.scanPhyloQTL.Rd qtl/man/movemarker.Rd qtl/man/geno.table.Rd qtl/man/interpPositions.Rd qtl/man/find.markerpos.Rd qtl/man/find.pseudomarker.Rd qtl/man/c.cross.Rd qtl/man/table2map.Rd qtl/man/drop.markers.Rd qtl/man/switch.order.Rd qtl/man/convert2riself.Rd qtl/man/comparecrosses.Rd qtl/man/mqmautocofactors.Rd qtl/man/nmissing.Rd qtl/man/map2table.Rd qtl/man/summary.map.Rd qtl/man/cbind.scanoneperm.Rd qtl/man/subset.scanone.Rd qtl/man/convert.map.Rd qtl/man/plot.pxg.Rd qtl/man/strip.partials.Rd qtl/man/summary.ripple.Rd qtl/man/scanqtl.Rd qtl/man/a.starting.point.Rd qtl/man/clean.cross.Rd qtl/man/stepwiseqtl.Rd qtl/man/mapthis.Rd qtl/man/ripple.Rd qtl/man/shiftmap.Rd qtl/man/addloctocross.Rd qtl/man/hyper.Rd qtl/man/scanonevar.varperm.Rd qtl/man/plot.cross.Rd qtl/man/mqmplotmultitrait.Rd qtl/man/badorder.Rd qtl/man/addcovarint.Rd qtl/man/findmarkerindex.Rd qtl/man/replacemap.scanone.Rd qtl/man/plot.geno.Rd qtl/man/addtoqtl.Rd qtl/man/max.scantwo.Rd qtl/man/xaxisloc.scanone.Rd qtl/man/groupclusteredheatmap.Rd qtl/man/plot.scanone.Rd qtl/man/reduce2grid.Rd qtl/man/transformPheno.Rd qtl/man/refineqtl.Rd qtl/man/countXO.Rd qtl/man/pull.rf.Rd qtl/man/pull.map.Rd qtl/man/effectplot.Rd qtl/man/summary.scanPhyloQTL.Rd qtl/man/scanoneboot.Rd qtl/man/checkAlleles.Rd qtl/man/mqmfind.marker.Rd qtl/man/subset.cross.Rd qtl/man/findDupMarkers.Rd qtl/man/sim.geno.Rd qtl/man/formLinkageGroups.Rd qtl/man/pickMarkerSubset.Rd qtl/man/fake.f2.Rd qtl/man/map10.Rd qtl/man/replace.map.Rd qtl/man/chrnames.Rd qtl/man/fake.bc.Rd qtl/man/readMWril.Rd qtl/man/switchAlleles.Rd qtl/man/plot.scanoneboot.Rd qtl/man/listeria.Rd qtl/man/summary.cross.Rd qtl/man/comparegeno.Rd qtl/man/pull.argmaxgeno.Rd qtl/man/dropfromqtl.Rd qtl/man/calc.errorlod.Rd qtl/man/simulateMissingData.Rd qtl/man/scantwopermhk.Rd qtl/man/summary.scantwoperm.Rd qtl/man/est.rf.Rd qtl/man/mqmaugment.Rd qtl/man/qtlversion.Rd qtl/man/droponemarker.Rd qtl/man/summary.scanone.Rd qtl/man/mqmpermutation.Rd qtl/man/fitstahl.Rd qtl/man/c.scantwo.Rd qtl/man/mqmplotcircle.Rd qtl/man/find.flanking.Rd qtl/man/flip.order.Rd qtl/man/plot.pheno.Rd qtl/man/geno.image.Rd qtl/man/lodint.Rd qtl/man/c.scanoneperm.Rd qtl/man/top.errorlod.Rd qtl/man/drop.dupmarkers.Rd qtl/man/subset.map.Rd qtl/man/formMarkerCovar.Rd qtl/man/plot.rf.Rd qtl/man/add.cim.covar.Rd qtl/man/fill.geno.Rd qtl/man/plot.scanPhyloQTL.Rd qtl/man/max.scanone.Rd qtl/man/chrlen.Rd qtl/man/rescalemap.Rd qtl/man/summary.fitqtl.Rd qtl/man/c.scantwoperm.Rd qtl/man/write.cross.Rd qtl/man/inferredpartitions.Rd qtl/man/subset.scanoneperm.Rd qtl/man/addpair.Rd qtl/man/mqmplotcistrans.Rd qtl/man/convert.scantwo.Rd qtl/man/reorderqtl.Rd qtl/man/nchr.Rd qtl/man/nqrank.Rd qtl/man/pull.draws.Rd qtl/man/pull.genoprob.Rd qtl/man/clean.scantwo.Rd qtl/man/arithscan.Rd qtl/man/sim.map.Rd qtl/man/mqmsetcofactors.Rd qtl/man/MQM.Rd qtl/man/phenames.Rd qtl/man/nullmarkers.Rd qtl/man/fitqtl.Rd qtl/man/plot.info.Rd qtl/man/plot.scanoneperm.Rd qtl/man/cbind.scantwoperm.Rd qtl/man/ntyped.Rd qtl/man/plot.missing.Rd qtl/man/addint.Rd qtl/man/find.pheno.Rd qtl/man/calc.penalties.Rd qtl/man/read.cross.Rd qtl/man/mqmextractmarkers.Rd qtl/man/plot.map.Rd qtl/man/effectscan.Rd qtl/man/fake.4way.Rd qtl/man/typingGap.Rd qtl/man/locateXO.Rd qtl/man/mqmscanfdr.Rd qtl/man/plot.rfmatrix.Rd qtl/man/mqmscanall.Rd qtl/man/arithscanperm.Rd qtl/man/locations.Rd qtl/man/simFounderSnps.Rd qtl/man/addqtl.Rd qtl/man/convert2risib.Rd qtl/man/convert.scanone.Rd qtl/man/mqmprocesspermutation.Rd qtl/man/c.scanone.Rd qtl/man/calc.genoprob.Rd qtl/man/sim.cross.Rd qtl/man/plotLodProfile.Rd qtl/man/jittermap.Rd qtl/man/cim.Rd qtl/man/allchrsplits.Rd qtl/man/mqmplotsingletrait.Rd qtl/man/subset.scantwoperm.Rd qtl/man/find.marker.Rd qtl/man/argmax.geno.Rd qtl/man/qtl-internal.Rd qtl/man/mqmplotcofactors.Rd qtl/man/scanone.Rd

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