Entry: vbscan
Aliases: vbscan
Keywords: models regression
Description: Genome scan for trait with some undefined values
URL: ../../../library/qtl/html/vbscan.html

Entry: read.cross.mm
Aliases: read.cross.mm
Keywords: file
Description: Read data for a QTL experiment in mapmaker format
URL: ../../../library/qtl/html/read.cross.mm.html

Entry: read.cross.gary
Aliases: read.cross.gary
Keywords: file
Description: Read data for a QTL experiment in Gary Churchill's format
URL: ../../../library/qtl/html/read.cross.gary.html

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

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

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

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

Entry: read.cross
Aliases: read.cross
Keywords: file
Description: Read data for a QTL experiment
URL: ../../../library/qtl/html/read.cross.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: scanone
Aliases: scanone
Keywords: models regression
Description: Genome scan with single QTL model
URL: ../../../library/qtl/html/scanone.html

Entry: plot.scanone
Aliases: plot.scanone
Keywords: hplot
Description: Plot output for a single QTL scan
URL: ../../../library/qtl/html/plot.scanone.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: drop.markers
Aliases: drop.markers
Keywords: manip
Description: Drop a set of markers
URL: ../../../library/qtl/html/drop.markers.html

Entry: top.errorlod
Aliases: top.errorlod
Keywords: manip
Description: List genotypes with highest error LOD values
URL: ../../../library/qtl/html/top.errorlod.html

Entry: plot.errors
Aliases: plot.errors
Keywords: hplot
Description: Plot grid of likely genotyping errors
URL: ../../../library/qtl/html/plot.errors.html

Entry: read.cross.csv
Aliases: read.cross.csv
Keywords: file
Description: Read data for a QTL experiment in comma-delimited format
URL: ../../../library/qtl/html/read.cross.csv.html

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

Entry: write.cross.mm
Aliases: write.cross.mm
Keywords: file
Description: Write data in mapmaker format
URL: ../../../library/qtl/html/write.cross.mm.html

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

Entry: vbscan.perm
Aliases: vbscan.perm
Keywords: models regression
Description: Permutation test for trait with some undefined values
URL: ../../../library/qtl/html/vbscan.perm.html

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

Entry: pull.chr
Aliases: pull.chr
Keywords: manip
Description: Pull out a subset of chromosomes from a cross
URL: ../../../library/qtl/html/pull.chr.html

Entry: plot.geno
Aliases: plot.geno
Keywords: hplot
Description: Plot genotypes with indication of likely errors
URL: ../../../library/qtl/html/plot.geno.html

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

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

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

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

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

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

Entry: read.cross.karl
Aliases: read.cross.karl
Keywords: file
Description: Read data for a QTL experiment in Karl Broman's format
URL: ../../../library/qtl/html/read.cross.karl.html

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

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

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

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

Entry: summary.scanone
Aliases: summary.scanone
Keywords: print
Description: Print summary of the scanone output
URL: ../../../library/qtl/html/summary.scanone.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.map
Aliases: plot.map
Keywords: hplot
Description: Plot genetic map
URL: ../../../library/qtl/html/plot.map.html

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

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

Entry: scanone.perm
Aliases: scanone.perm
Keywords: models regression
Description: Permutation test for genome scan with single QTL model
URL: ../../../library/qtl/html/scanone.perm.html

Entry: write.cross.csv
Aliases: write.cross.csv
Keywords: file
Description: Write data in comma-delimited format
URL: ../../../library/qtl/html/write.cross.csv.html

Entry: plot.rf
Aliases: plot.rf
Keywords: hplot
Description: Plot recombination fractions
URL: ../../../library/qtl/html/plot.rf.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: clean
Aliases: clean
Keywords: manip
Description: Remove intermediate calculations
URL: ../../../library/qtl/html/clean.html

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

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

Entry: convert2ss
Aliases: convert2ss
Keywords: manip
Description: Convert an intercross into a form to allow sex-specific maps
URL: ../../../library/qtl/html/convert2ss.html

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

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

Entry: drop.qtlgeno
Aliases: drop.qtlgeno
Keywords: manip
Description: Remove QTL genotypes
URL: ../../../library/qtl/html/drop.qtlgeno.html

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

