qtl

Introduction to Multiple QTL Model (MQM) mapping

Introductory comments on R/qtl

Indicate marker covariates from composite interval mapping

Add significance threshold to plot

Add QTL x covariate interaction to a multiple-QTL model

Add pairwise interaction to a multiple-QTL model

Add phenotype location into a cross object

Add a marker to a cross

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

Scan for an additional QTL in a multiple-QTL model

Add to a qtl object

Test all possible splits of a chromosome into two pieces

Reconstruct underlying genotypes

Arithmetic operators for scanone and scantwo results

Arithmetic Operators for permutation results

An intercross with misplaced markers

Bayesian credible interval

Data on bristle number in Drosophila

Data on bristle number in Drosophila

Combine data for QTL experiments

Combine columns from multiple scanone results

Combine data from scanone permutations

Combine columns from multiple scantwo results

Combine data from scantwo permutations

Identify likely genotyping errors

Calculate conditional genotype probabilities

Calculate LOD penalties

Combine columns from multiple scanone permutation results

Combine scantwo permutations by column

Identify markers with switched alleles

Chromosome lengths in QTL experiment

Pull out the chromosome names from a cross

Composite interval mapping

Remove derived data

Clean up scantwo output

Delete genotypes that are possibly in error

Compare two cross objects

Compare individuals' genotype data

Compare two orderings of markers on a chromosome

Condense the output from a 2-d genome scan

Change map function for a genetic map

Convert output from scanone for R/qtl version 0.98

Convert output from scantwo for R/qtl version 1.03 and earlier

Convert a cross to RIL by selfing

Convert a cross to RIL by sib mating

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

Count number of obligate crossovers for each individual

Drop duplicate markers

Drop a set of markers

Drop markers without any genotype data

Drop a QTL from a qtl object

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

Plot phenotype means against genotypes at one or two markers

Plot estimated QTL effects across the whole genome

Estimate genetic maps

Estimate pairwise recombination fractions

Simulated data for a 4-way cross

Simulated data for a backcross

Simulated data for an F2 intercross

Fill holes in genotype data

Find flanking markers for a specified position

Find marker closest to a specified position

Find position of a marker

Find column number for a particular phenotype

Find the pseudomarker closest to a specified position

Find markers with identical genotype data

Find large intervals in a map

Determine the numeric index for a marker

Fit a multiple-QTL model

Fit Stahl interference model

Flip the orders of markers on a set of chromosomes

Partition markers into linkage groups

Create matrix of marker covariates for QTL analysis

Create table of two-locus genotypes

Plot grid of genotype data

Create table of genotype distributions

Pull out the individual identifiers from a cross

Retrieving groups of traits after clustering

Data on hypertension

Crude reconstruction of founder haplotypes in multi-parent RIL

Identify inferred partitions in mapping QTL to a phylogenetic tree

Interpolate positions from one map to another

Jitter marker positions in a genetic map

Data on Listeria monocytogenes susceptibility

Estimate locations of crossovers

Genetic locations of traits for the multitrait dataset

LOD support interval

Make a qtl object

An example genetic map

Convert genetic map from list to table.

Simulated data for illustrating genetic map construction

General likelihood ratio test for association between marker pairs

Pull out the marker names from a cross

Maximum peak in genome scan to map a QTL to a phylogenetic tree

Maximum peak in genome scan

Maximum peak in two-dimensional genome scan

Move a marker to a new chromosome

MQM augmentation

Automatic setting of cofactors, taking marker density into account

MQM marker extraction

Fetch significant markers after permutation analysis

Retrieve the QTL model used in mapping from the results of an MQM scan

Estimate QTL LOD score significance using permutations or simulations

Circular genome plot for MQM

cis-trans plot

Plot clustered heatmap of MQM scan on multiple phenotypes

Plot cofactors on the genetic map

Plot LOD*Effect curves of a multiple-QTL model

Heatmap of a genome of MQM scan on multiple phenotypes

Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes

Plot results from mqmpermutation

Plot LOD curves of a multiple-QTL model

Convert mqmmulti objects into a scanoneperm object

Genome scan with a multiple QTL model (MQM)

Parallelized MQM on multiple phenotypes in a cross object

Estimate FDR for multiple trait QTL analysis

Set cofactors at fixed intervals, to be used with MQM

Shapiro normality test used for MQM

Example Cross object from R/QTL with multiple traits

Determine the number of chromosomes

Determine the number of individuals QTL experiment

Determine the numbers of markers on each chromosome

Number of missing genotypes

Determine the number of phenotypes QTL experiment

Transform a vector of quantitative values to the corresponding normal quantiles

Determine the number of QTL in a QTL object

Number of genotypes

Identify markers without any genotype data

Find an initial order for markers within chromosomes

Pull out the phenotypes names from a cross

Identify the largest subset of markers that are some distance apart

Plot genotype comparison

Plot various features of a cross object

Plot grid of error LOD values

Plot observed genotypes, flagging likely errors

Plot the proportion of missing genotype information

Plot genetic map

Plot grid of missing genotypes

Plot a phenotype distribution

Plot phenotypes versus marker genotypes

Plot QTL locations

Plot recombination fractions

Plot recombination fractions or LOD scores for a single marker

Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree

Plot LOD curves

Plot results of bootstrap for QTL position

Plot permutation results for a single-QTL genome scan

Plot LOD scores for a two-dimensional genome scan

Plot permutation results for a 2d, 2-QTL genome scan

Plot 1-d LOD profiles for a multiple QTL model

Plot a QTL model

Pull out the results of the Viterbi algorithm from a cross

Pull out the genotype imputations from a cross

Pull out the genotype data from a cross

Pull out the genotype probabilities from a cross

Pull out the genetic map from a cross

Drop all but a selected set of markers

Pull out phenotype data from a cross

Pull out recombination fractions or LOD scores from a cross object

Internal qtl functions

Installed version of R/qtl

Read data for a QTL experiment

Read data for 4- or 8-way RIL

Reduce to a grid of pseudomarkers.

Refine the positions of QTL

Reorder the QTL in a qtl object

Replace the genetic map of a cross

Replace the genetic map in QTL mapping results with an alternate map

Replace the genetic map in QTL mapping results with an alternate map

Replace a QTL in a qtl object with a different position

Rescale genetic maps

Compare marker orders

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

Genome scan with a single QTL model

Bootstrap to get interval estimate of QTL location

Genome scan for QTL affecting mean and/or variance

Permutation test for mean effect in scanonevar

Permutation test for variance effect in scanonevar

General QTL scan

Two-dimensional genome scan with a two-QTL model

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

Shift starting points in genetic maps

Simulate a QTL experiment

Simulate genotypes given observed marker data

Simulate a genetic map

Simulate founder SNPs for a multiple-strain RIL

Simulate a set of intercrosses for a single diallelic QTL

Simulates missing genotype data

Stepwise selection for multiple QTL

Strip partially informative genotypes

Subsetting data for QTL experiment

Subsetting chromosomes for a genetic map

Subsetting the results of a genome scan

Subsetting permutation test results

Subsetting the results of a 2-d genome scan

Subsetting two-dimensional permutation test results

Print pairs of individuals with similar genotype data.

Print summary of QTL experiment

Summary of fit of qtl model

Print summary of a genetic map

Print summary of a QTL object

Print summary of ripple results

Summarize the results a genome scan to map a QTL to a phylogenetic tree

Summarize the results of a genome scans

Bootstrap confidence interval for QTL location

LOD thresholds from scanone permutation results

Summarize the results of a two-dimensional genome scan

Summarize the results of a two-dimensional genome scan

LOD thresholds from scantwo permutation results

Switch the order of markers on a chromosome

Switch alleles at selected markers

Convert a table of marker positions to a map object.

List genotypes with large error LOD scores

Determine the total number of markers

Transformation of the phenotypes in a cross object

Test all possible positions for a marker

Maximum distance between genotyped markers

Write data for a QTL experiment to a file

Get x-axis locations in scanone plot