Introduction to Multiple QTL Model (MQM) mapping
Scan for an additional pair of QTL in a multiple-QTL model
Add significance threshold to plot
Add pairwise interaction to a multiple-QTL model
Indicate marker covariates from composite interval mapping
Add phenotype location into a cross object
Add a marker to a cross
Scan for an additional QTL in a multiple-QTL model
Add QTL x covariate interaction to a multiple-QTL model
Introductory comments on R/qtl
Data on bristle number in Drosophila
Identify likely genotyping errors
Combine columns from multiple scantwo results
Combine scantwo permutations by column
Combine columns from multiple scanone permutation results
Bayesian credible interval
Arithmetic Operators for permutation results
Test all possible splits of a chromosome into two pieces
Data on bristle number in Drosophila
Arithmetic operators for scanone and scantwo results
Combine columns from multiple scanone results
An intercross with misplaced markers
Combine data for QTL experiments
Calculate conditional genotype probabilities
Add to a qtl object
Clean up scantwo output
Compare two orderings of markers on a chromosome
Remove derived data
Chromosome lengths in QTL experiment
Composite interval mapping
Identify markers with switched alleles
Compare two cross objects
Delete genotypes that are possibly in error
Reconstruct underlying genotypes
Combine data from scanone permutations
Calculate LOD penalties
Combine data from scantwo permutations
Compare individuals' genotype data
Estimate genetic maps
Count number of obligate crossovers for each individual
Convert a sex-specific map to a sex-averaged one
Drop a QTL from a qtl object
Fill holes in genotype data
Pull out the chromosome names from a cross
Plot estimated QTL effects across the whole genome
Change map function for a genetic map
Drop markers without any genotype data
Drop a set of markers
Convert a cross to RIL by sib mating
Simulated data for a 4-way cross
Condense the output from a 2-d genome scan
Drop one marker at a time and determine effect on genetic map
Plot phenotype means against genotypes at one or two markers
Drop duplicate markers
Convert a cross to RIL by selfing
Convert output from scantwo for R/qtl version 1.03 and earlier
Convert output from scanone for R/qtl version 0.98
Simulated data for an F2 intercross
Simulated data for a backcross
Fit Stahl interference model
LOD support interval
Fit a multiple-QTL model
Estimate pairwise recombination fractions
Find markers with identical genotype data
Determine the numeric index for a marker
Find large intervals in a map
Create matrix of marker covariates for QTL analysis
Find position of a marker
Pull out the individual identifiers from a cross
Create table of genotype distributions
Retrieving groups of traits after clustering
Data on hypertension
An example genetic map
Find flanking markers for a specified position
Plot grid of genotype data
Find the pseudomarker closest to a specified position
Crude reconstruction of founder haplotypes in multi-parent RIL
Find column number for a particular phenotype
Create table of two-locus genotypes
Maximum peak in two-dimensional genome scan
Data on Listeria monocytogenes susceptibility
Automatic setting of cofactors, taking marker density into account
Estimate locations of crossovers
MQM marker extraction
Genetic locations of traits for the multitrait dataset
Make a qtl object
Convert genetic map from list to table.
Maximum peak in genome scan
Jitter marker positions in a genetic map
Find marker closest to a specified position
Move a marker to a new chromosome
Pull out the marker names from a cross
cis-trans plot
MQM augmentation
Flip the orders of markers on a set of chromosomes
General likelihood ratio test for association between marker pairs
Plot cofactors on the genetic map
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes
Plot LOD*Effect curves of a multiple-QTL model
Partition markers into linkage groups
Heatmap of a genome of MQM scan on multiple phenotypes
Set cofactors at fixed intervals, to be used with MQM
Plot clustered heatmap
of MQM scan on multiple phenotypes
Simulated data for illustrating genetic map construction
Shapiro normality test used for MQM
Determine the number of chromosomes
Convert mqmmulti objects into a scanoneperm object
Plot results from mqmpermutation
Estimate QTL LOD score significance using permutations or simulations
Genome scan with a multiple QTL model (MQM)
Interpolate positions from one map to another
Maximum peak in genome scan to map a QTL to a phylogenetic tree
Plot LOD curves of a multiple-QTL model
Number of genotypes
Determine the number of individuals QTL experiment
Determine the numbers of markers on each chromosome
Fetch significant markers after permutation analysis
Identify markers without any genotype data
Number of missing genotypes
Retrieve the QTL model used in mapping from the results of an MQM scan
Example Cross object from R/QTL with multiple traits
Identify inferred partitions in mapping QTL to a phylogenetic tree
Pull out the phenotypes names from a cross
Determine the number of QTL in a QTL object
Plot a phenotype distribution
Find an initial order for markers within chromosomes
Transform a vector of quantitative values to the corresponding
normal quantiles
Plot the proportion of missing genotype information
Determine the number of phenotypes QTL experiment
Plot phenotypes versus marker genotypes
Plot genetic map
Estimate FDR for multiple trait QTL analysis
Parallelized MQM on multiple phenotypes in a cross object
Plot observed genotypes, flagging likely errors
Circular genome plot for MQM
Plot QTL locations
Plot LOD scores for a two-dimensional genome scan
Plot grid of missing genotypes
Plot LOD curves
Plot grid of error LOD values
Plot genotype comparison
Plot various features of a cross object
Plot permutation results for a single-QTL genome scan
Identify the largest subset of markers that are some distance apart
Plot permutation results for a 2d, 2-QTL genome scan
Pull out the genotype imputations from a cross
Plot results of bootstrap for QTL position
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree
Plot recombination fractions or LOD scores for a single marker
Plot 1-d LOD profiles for a multiple QTL model
Drop all but a selected set of markers
Pull out phenotype data from a cross
Pull out the results of the Viterbi algorithm from a cross
Pull out recombination fractions or LOD scores from a cross object
Internal qtl functions
Pull out the genetic map from a cross
Plot recombination fractions
Pull out the genotype data from a cross
Plot a QTL model
Pull out the genotype probabilities from a cross
Reorder the QTL in a qtl object
Replace the genetic map of a cross
Installed version of R/qtl
Reduce to a grid of pseudomarkers.
Replace the genetic map in QTL mapping results with an alternate map
Replace a QTL in a qtl object with a different position
Replace the genetic map in QTL mapping results with an alternate map
Refine the positions of QTL
Read data for 4- or 8-way RIL
Read data for a QTL experiment
Permutation test for mean effect in scanonevar
Rescale genetic maps
Permutation test for variance effect in scanonevar
General QTL scan
Two-dimensional genome scan with a two-QTL model
Bootstrap to get interval estimate of QTL location
Compare marker orders
Genome scan for QTL affecting mean and/or variance
Single-QTL genome scan to map QTL to a phylogenetic tree
Genome scan with a single QTL model
Simulate founder SNPs for a multiple-strain RIL
Permutation test for 2d genome scan by Haley-Knott regression
Strip partially informative genotypes
Shift starting points in genetic maps
Simulates missing genotype data
Simulate a genetic map
Simulate genotypes given observed marker data
Stepwise selection for multiple QTL
Simulate a set of intercrosses for a single diallelic QTL
Simulate a QTL experiment
Summary of fit of qtl model
Print summary of QTL experiment
Subsetting the results of a 2-d genome scan
Subsetting the results of a genome scan
Subsetting data for QTL experiment
Subsetting permutation test results
Print pairs of individuals with similar genotype data.
Print summary of a genetic map
Subsetting two-dimensional permutation test results
Subsetting chromosomes for a genetic map
Summarize the results of a genome scans
Summarize the results a genome scan to map a QTL to a phylogenetic tree
Summarize the results of a two-dimensional genome scan
Print summary of ripple results
LOD thresholds from scantwo permutation results
Bootstrap confidence interval for QTL location
Switch the order of markers on a chromosome
Print summary of a QTL object
Summarize the results of a two-dimensional genome scan
LOD thresholds from scanone permutation results
Determine the total number of markers
Transformation of the phenotypes in a cross object
List genotypes with large error LOD scores
Write data for a QTL experiment to a file
Test all possible positions for a marker
Switch alleles at selected markers
Get x-axis locations in scanone plot
Maximum distance between genotyped markers
Convert a table of marker positions to a map object.