Entry: A starting point
Aliases: A starting point
Keywords: models
Description: Introductory comments
URL: ../../../library/qtl/html/a.starting.point.html

Entry: argmax.geno
Aliases: argmax.geno
Keywords: utilities
Description: Reconstruct underlying genotypes
URL: ../../../library/qtl/html/argmax.geno.html

Entry: arithscan
Aliases: +.scanone -.scanone +.scantwo -.scantwo
Keywords: arith
Description: Arithmetic Operators for scanone and scantwo results
URL: ../../../library/qtl/html/arithscan.html

Entry: arithscanperm
Aliases: +.scanoneperm -.scanoneperm +.scantwoperm -.scantwoperm
Keywords: arith
Description: Arithmetic Operators for permutation results
URL: ../../../library/qtl/html/arithscanperm.html

Entry: badorder
Aliases: badorder
Keywords: datasets
Description: An intercross with misplaced markers
URL: ../../../library/qtl/html/badorder.html

Entry: bayesint
Aliases: bayesint
Keywords: utilities
Description: Bayesian credible interval
URL: ../../../library/qtl/html/bayesint.html

Entry: bristle3
Aliases: bristle3
Keywords: datasets
Description: Data on bristle number in Drosophila
URL: ../../../library/qtl/html/bristle3.html

Entry: bristleX
Aliases: bristleX
Keywords: datasets
Description: Data on bristle number in Drosophila
URL: ../../../library/qtl/html/bristleX.html

Entry: c.cross
Aliases: c.cross
Keywords: manip
Description: Combine data for QTL experiments
URL: ../../../library/qtl/html/c.cross.html

Entry: c.scanone
Aliases: c.scanone
Keywords: manip
Description: Combine columns from multiple scanone results
URL: ../../../library/qtl/html/c.scanone.html

Entry: c.scanoneperm
Aliases: c.scanoneperm rbind.scanoneperm
Keywords: manip
Description: Combine data from scanone permutations
URL: ../../../library/qtl/html/c.scanoneperm.html

Entry: c.scantwoperm
Aliases: c.scantwoperm rbind.scantwoperm
Keywords: manip
Description: Combine data from scantwo permutations
URL: ../../../library/qtl/html/c.scantwoperm.html

Entry: calc.errorlod
Aliases: calc.errorlod
Keywords: utilities
Description: Identify likely genotyping errors
URL: ../../../library/qtl/html/calc.errorlod.html

Entry: calc.genoprob
Aliases: calc.genoprob
Keywords: utilities
Description: Calculate conditional genotype probabilities
URL: ../../../library/qtl/html/calc.genoprob.html

Entry: cbind.scanoneperm
Aliases: cbind.scanoneperm
Keywords: manip
Description: Combine columns from multiple scanone permutation results
URL: ../../../library/qtl/html/cbind.scanoneperm.html

Entry: checkAlleles
Aliases: checkAlleles
Keywords: utilities
Description: Identify markers with switched alleles
URL: ../../../library/qtl/html/checkAlleles.html

Entry: chrlen
Aliases: chrlen
Keywords: print
Description: Chromosome lengths in QTL experiment
URL: ../../../library/qtl/html/chrlen.html

Entry: clean.cross
Aliases: clean.cross
Keywords: manip
Description: Remove derived data
URL: ../../../library/qtl/html/clean.cross.html

Entry: clean.scantwo
Aliases: clean.scantwo
Keywords: manip
Description: Clean up scantwo output
URL: ../../../library/qtl/html/clean.scantwo.html

Entry: comparecrosses
Aliases: comparecrosses
Keywords: utilities
Description: Compare two cross objects.
URL: ../../../library/qtl/html/comparecrosses.html

Entry: comparegeno
Aliases: comparegeno
Keywords: utilities
Description: Compare individuals' genotype data
URL: ../../../library/qtl/html/comparegeno.html

Entry: condense.scantwo
Aliases: condense.scantwo
Keywords: print
Description: Condense the output from a 2-d genome scan
URL: ../../../library/qtl/html/condense.scantwo.html

Entry: convert.scanone
Aliases: convert.scanone
Keywords: manip
Description: Convert output from scanone for R/qtl version 0.98
URL: ../../../library/qtl/html/convert.scanone.html

Entry: convert.scantwo
Aliases: convert.scantwo
Keywords: manip
Description: Convert output from scantwo for R/qtl version 1.03 and earlier
URL: ../../../library/qtl/html/convert.scantwo.html

Entry: drop.markers
Aliases: drop.markers
Keywords: manip
Description: Drop a set of markers
URL: ../../../library/qtl/html/drop.markers.html

Entry: drop.nullmarkers
Aliases: drop.nullmarkers
Keywords: manip
Description: Drop markers without any genotype data
URL: ../../../library/qtl/html/drop.nullmarkers.html

Entry: effectplot
Aliases: effectplot
Keywords: hplot
Description: Plot phenotype means against genotypes at one or two markers.
URL: ../../../library/qtl/html/effectplot.html

Entry: effectscan
Aliases: effectscan
Keywords: hplot
Description: Plot allelic effect across the whole genome
URL: ../../../library/qtl/html/effectscan.html

Entry: est.map
Aliases: est.map
Keywords: utilities
Description: Estimate genetic maps
URL: ../../../library/qtl/html/est.map.html

Entry: est.rf
Aliases: est.rf
Keywords: utilities
Description: Estimate pairwise recombination fractions
URL: ../../../library/qtl/html/est.rf.html

Entry: fake.4way
Aliases: fake.4way
Keywords: datasets
Description: Simulated data for a 4-way cross
URL: ../../../library/qtl/html/fake.4way.html

Entry: fake.bc
Aliases: fake.bc
Keywords: datasets
Description: Simulated data for a backcross
URL: ../../../library/qtl/html/fake.bc.html

Entry: fake.f2
Aliases: fake.f2
Keywords: datasets
Description: Simulated data for an F2 intercross
URL: ../../../library/qtl/html/fake.f2.html

Entry: fill.geno
Aliases: fill.geno
Keywords: utilities
Description: Fill holes in genotype data
URL: ../../../library/qtl/html/fill.geno.html

Entry: find.flanking
Aliases: find.flanking
Keywords: utilities
Description: Find flanking markers for a specified position
URL: ../../../library/qtl/html/find.flanking.html

Entry: find.marker
Aliases: find.marker
Keywords: utilities
Description: Find marker closest to a specified position
URL: ../../../library/qtl/html/find.marker.html

Entry: find.pheno
Aliases: find.pheno
Keywords: utilities
Description: Find column number for a particular phenotype.
URL: ../../../library/qtl/html/find.pheno.html

Entry: find.pseudomarker
Aliases: find.pseudomarker
Keywords: utilities
Description: Find the pseudomarker closest to a specified position
URL: ../../../library/qtl/html/find.pseudomarker.html

Entry: fitqtl
Aliases: fitqtl
Keywords: models
Description: Fit a multiple-QTL model
URL: ../../../library/qtl/html/fitqtl.html

Entry: fitstahl
Aliases: fitstahl
Keywords: models
Description: Fit Stahl interference model
URL: ../../../library/qtl/html/fitstahl.html

Entry: geno.table
Aliases: geno.table
Keywords: utilities
Description: Create table of genotype distributions
URL: ../../../library/qtl/html/geno.table.html

Entry: hyper
Aliases: hyper
Keywords: datasets
Description: Data on hypertension
URL: ../../../library/qtl/html/hyper.html

Entry: jittermap
Aliases: jittermap
Keywords: manip
Description: Jitter marker positions in a genetic map
URL: ../../../library/qtl/html/jittermap.html

Entry: listeria
Aliases: listeria
Keywords: datasets
Description: Data on Listeria monocytogenes susceptibility
URL: ../../../library/qtl/html/listeria.html

Entry: lodint
Aliases: lodint
Keywords: utilities
Description: LOD support interval
URL: ../../../library/qtl/html/lodint.html

Entry: makeqtl
Aliases: makeqtl
Keywords: utilities
Description: Make a qtl object
URL: ../../../library/qtl/html/makeqtl.html

Entry: map10
Aliases: map10
Keywords: datasets
Description: An example genetic map
URL: ../../../library/qtl/html/map10.html

Entry: max.scanone
Aliases: max.scanone
Keywords: print
Description: Maximum peak in genome scan
URL: ../../../library/qtl/html/max.scanone.html

Entry: max.scantwo
Aliases: max.scantwo
Keywords: print
Description: Maximum peak in two-dimensional genome scan
URL: ../../../library/qtl/html/max.scantwo.html

Entry: movemarker
Aliases: movemarker
Keywords: manip
Description: Move a marker to a new chromosome
URL: ../../../library/qtl/html/movemarker.html

Entry: nmissing
Aliases: nmissing
Keywords: utilities
Description: Number of missing genotypes
URL: ../../../library/qtl/html/nmissing.html

Entry: plot.cross
Aliases: plot.cross
Keywords: hplot
Description: Plot various features of a cross object
URL: ../../../library/qtl/html/plot.cross.html

Entry: plot.errorlod
Aliases: plot.errorlod
Keywords: hplot
Description: Plot grid of error LOD values
URL: ../../../library/qtl/html/plot.errorlod.html

Entry: plot.geno
Aliases: plot.geno
Keywords: hplot
Description: Plot observed genotypes, flagging likely errors
URL: ../../../library/qtl/html/plot.geno.html

Entry: plot.info
Aliases: plot.info
Keywords: hplot univar
Description: Plot the proportion of missing genotype information
URL: ../../../library/qtl/html/plot.info.html

Entry: plot.map
Aliases: plot.map
Keywords: hplot
Description: Plot genetic map
URL: ../../../library/qtl/html/plot.map.html

Entry: plot.missing
Aliases: plot.missing
Keywords: hplot
Description: Plot grid of missing genotypes
URL: ../../../library/qtl/html/plot.missing.html

Entry: plot.pheno
Aliases: plot.pheno
Keywords: hplot
Description: Plot a phenotype distribution
URL: ../../../library/qtl/html/plot.pheno.html

Entry: plot.pxg
Aliases: plot.pxg
Keywords: hplot
Description: Plot phenotypes versus marker genotypes.
URL: ../../../library/qtl/html/plot.pxg.html

Entry: plot.rf
Aliases: plot.rf
Keywords: hplot
Description: Plot recombination fractions
URL: ../../../library/qtl/html/plot.rf.html

Entry: plot.scanone
Aliases: plot.scanone
Keywords: hplot
Description: Plot LOD curves
URL: ../../../library/qtl/html/plot.scanone.html

Entry: plot.scantwo
Aliases: plot.scantwo
Keywords: hplot
Description: Plot LOD scores for a two-dimensional genome scan
URL: ../../../library/qtl/html/plot.scantwo.html

Entry: pull.geno
Aliases: pull.geno
Keywords: utilities
Description: Pull out the genotype data from a cross
URL: ../../../library/qtl/html/pull.geno.html

Entry: pull.map
Aliases: pull.map
Keywords: utilities
Description: Pull out the genetic map from a cross
URL: ../../../library/qtl/html/pull.map.html

Entry: qtl-internal
Aliases: addqtl adjust.rf.ri calc.pairprob checkcovar clean condense convert create.map discan dropqtl dropXcol effectplot.getmark effectplot.calmeanse fitstahl.estp fitstahl.este fitstahl.estpe fitstahl.estp.sub fitstahl.este.sub fitstahl.estpe.sub fixX4write fixXgeno.bc fixXgeno.f2 getid getsex getgenonames grab.arg.names imf.cf imf.h imf.k imf.m imf.stahl locatemarker locate.xo makeSSmap max.scantwocondensed mf.cf mf.h mf.k mf.m mf.stahl parseformula print.cross print.map print.scantwo print.summary.cross print.summary.fitqtl print.summary.map print.summary.ripple print.summary.scanone print.summary.scanoneperm print.summary.scantwo print.summary.scantwo.old print.summary.scantwoperm read.cro.qtlcart read.cross.csv read.cross.csvs read.cross.gary read.cross.karl read.cross.mm read.cross.qtlcart read.cross.qtx read.map.qtlcart read.maps.mm replaceqtl revisecovar revisescantwodf reviseXdata ripple.perm1 ripple.perm2 ripple.perm.sub scanone.perm scanone.perm.engine scanoneXnull scantwo.perm scantwo.perm.engine sim.bcg sim.cc sim.cross.4way sim.cross.bc sim.cross.f2 sim.ril subrousummaryscantwo summary.scantwocondensed vbscan write.cross.csv write.cross.gary write.cross.mm write.cross.qtlcart
Keywords: internal
Description: Internal qtl functions
URL: ../../../library/qtl/html/qtl-internal.html

Entry: qtlversion
Aliases: qtlversion
Keywords: print
Description: Installed version of R/qtl
URL: ../../../library/qtl/html/qtlversion.html

Entry: read.cross
Aliases: read.cross
Keywords: IO
Description: Read data for a QTL experiment
URL: ../../../library/qtl/html/read.cross.html

Entry: replace.map
Aliases: replace.map
Keywords: manip
Description: Replace the genetic map of a cross
URL: ../../../library/qtl/html/replace.map.html

Entry: ripple
Aliases: ripple
Keywords: utilities
Description: Compare marker orders
URL: ../../../library/qtl/html/ripple.html

Entry: scanone
Aliases: scanone
Keywords: models
Description: Genome scan with a single QTL model
URL: ../../../library/qtl/html/scanone.html

Entry: scanqtl
Aliases: scanqtl
Keywords: models
Description: General QTL scan
URL: ../../../library/qtl/html/scanqtl.html

Entry: scantwo
Aliases: scantwo
Keywords: models
Description: Two-dimensional genome scan with a two-QTL model
URL: ../../../library/qtl/html/scantwo.html

Entry: sim.cross
Aliases: sim.cross
Keywords: datagen
Description: Simulate a QTL experiment
URL: ../../../library/qtl/html/sim.cross.html

Entry: sim.geno
Aliases: sim.geno
Keywords: utilities
Description: Simulate genotypes given observed marker data
URL: ../../../library/qtl/html/sim.geno.html

Entry: sim.map
Aliases: sim.map
Keywords: datagen
Description: Simulate a genetic map
URL: ../../../library/qtl/html/sim.map.html

Entry: strip.partials
Aliases: strip.partials
Keywords: manip
Description: Strip partially informative genotypes
URL: ../../../library/qtl/html/strip.partials.html

Entry: subset.cross
Aliases: subset.cross
Keywords: manip
Description: Subsetting data for QTL experiment
URL: ../../../library/qtl/html/subset.cross.html

Entry: subset.scanone
Aliases: subset.scanone
Keywords: manip
Description: Subsetting the results of a genome scan
URL: ../../../library/qtl/html/subset.scanone.html

Entry: subset.scantwo
Aliases: subset.scantwo
Keywords: manip
Description: Subsetting the results of a 2-d genome scan
URL: ../../../library/qtl/html/subset.scantwo.html

Entry: summary.cross
Aliases: summary.cross nind nmar totmar nchr nphe
Keywords: print
Description: Print summary of QTL experiment
URL: ../../../library/qtl/html/summary.cross.html

Entry: summary.fitqtl
Aliases: summary.fitqtl
Keywords: print
Description: Summary of fit of qtl model
URL: ../../../library/qtl/html/summary.fitqtl.html

Entry: summary.map
Aliases: summary.map
Keywords: print
Description: Print summary of a genetic map
URL: ../../../library/qtl/html/summary.map.html

Entry: summary.ripple
Aliases: summary.ripple
Keywords: print
Description: Print summary of ripple results
URL: ../../../library/qtl/html/summary.ripple.html

Entry: summary.scanone
Aliases: summary.scanone
Keywords: print
Description: Summarize the results of a genome scans
URL: ../../../library/qtl/html/summary.scanone.html

Entry: summary.scanoneperm
Aliases: summary.scanoneperm
Keywords: print
Description: LOD thresholds from scanone permutation results
URL: ../../../library/qtl/html/summary.scanoneperm.html

Entry: summary.scantwo
Aliases: summary.scantwo
Keywords: print
Description: Summarize the results of a two-dimensional genome scan
URL: ../../../library/qtl/html/summary.scantwo.html

Entry: summary.scantwo.old
Aliases: summary.scantwo.old
Keywords: print
Description: Summarize the results of a two-dimensional genome scan
URL: ../../../library/qtl/html/summary.scantwo.old.html

Entry: summary.scantwoperm
Aliases: summary.scantwoperm
Keywords: print
Description: LOD thresholds from scantwo permutation results
URL: ../../../library/qtl/html/summary.scantwoperm.html

Entry: switch.order
Aliases: switch.order
Keywords: manip
Description: Switch the order of markers on a chromosome
URL: ../../../library/qtl/html/switch.order.html

Entry: top.errorlod
Aliases: top.errorlod
Keywords: print
Description: List genotypes with large error LOD scores
URL: ../../../library/qtl/html/top.errorlod.html

Entry: write.cross
Aliases: write.cross
Keywords: IO
Description: Write data for a QTL experiment to a file
URL: ../../../library/qtl/html/write.cross.html
