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