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qtl (version 1.39-5)

Tools for Analyzing QTL Experiments

Description

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.

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Version

Install

install.packages('qtl')

Monthly Downloads

4,141

Version

1.39-5

License

GPL-3

Maintainer

Karl W Broman

Last Published

March 4th, 2016

Functions in qtl (1.39-5)

checkAlleles

Identify markers with switched alleles

max.scantwo

Maximum peak in two-dimensional genome scan

nmar

Determine the numbers of markers on each chromosome

scanonevar

Genome scan for QTL affecting mean and/or variance

A starting point

Introductory comments on R/qtl

convert2riself

Convert a cross to RIL by selfing

chrnames

Pull out the chromosome names from a cross

scanone

Genome scan with a single QTL model

markerlrt

General likelihood ratio test for association between marker pairs

add.threshold

Add significance threshold to plot

plot.scanoneboot

Plot results of bootstrap for QTL position

compareorder

Compare two orderings of markers on a chromosome

est.map

Estimate genetic maps

top.errorlod

List genotypes with large error LOD scores

multitrait

Example Cross object from R/QTL with multiple traits

write.cross

Write data for a QTL experiment to a file

dropfromqtl

Drop a QTL from a qtl object

fake.f2

Simulated data for an F2 intercross

mqmplot.singletrait

Plot LOD curves of a multiple-QTL model

transformPheno

Transformation of the phenotypes in a cross object

mqmscanfdr

Estimate FDR for multiple trait QTL analysis

convert2risib

Convert a cross to RIL by sib mating

argmax.geno

Reconstruct underlying genotypes

plot.scanone

Plot LOD curves

fitqtl

Fit a multiple-QTL model

plotErrorlod

Plot grid of error LOD values

lodint

LOD support interval

plotRF

Plot recombination fractions

comparecrosses

Compare two cross objects

formLinkageGroups

Partition markers into linkage groups

totmar

Determine the total number of markers

getid

Pull out the individual identifiers from a cross

replacemap.scanone

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

cim

Composite interval mapping

map2table

Convert genetic map from list to table.

addcovarint

Add QTL x covariate interaction to a multiple-QTL model

mapthis

Simulated data for illustrating genetic map construction

badorder

An intercross with misplaced markers

pull.pheno

Pull out phenotype data from a cross

formMarkerCovar

Create matrix of marker covariates for QTL analysis

c.scanoneperm

Combine data from scanone permutations

find.markerindex

Determine the numeric index for a marker

clean.scantwo

Clean up scantwo output

calc.errorlod

Identify likely genotyping errors

c.scantwo

Combine columns from multiple scantwo results

addmarker

Add a marker to a cross

ripple

Compare marker orders

qtlversion

Installed version of R/qtl

clean.cross

Remove derived data

drop.nullmarkers

Drop markers without any genotype data

Bootstrap confidence interval for QTL location

fake.bc

Simulated data for a backcross

condense.scantwo

Condense the output from a 2-d genome scan

convert2sa

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

max.scanone

Maximum peak in genome scan

mqmfind.marker

Fetch significant markers after permutation analysis

geno.image

Plot grid of genotype data

find.pheno

Find column number for a particular phenotype

summaryScantwoOld

Summarize the results of a two-dimensional genome scan

mqmplot.clusteredheatmap

Plot clustered heatmap of MQM scan on multiple phenotypes

convert.scanone

Convert output from scanone for R/qtl version 0.98

plotInfo

Plot the proportion of missing genotype information

findDupMarkers

Find markers with identical genotype data

drop.markers

Drop a set of markers

MQM

Introduction to Multiple QTL Model (MQM) mapping

table2map

Convert a table of marker positions to a map object.

max.scanPhyloQTL

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

qtl-internal

Internal qtl functions

effectplot

Plot phenotype means against genotypes at one or two markers

read.cross

Read data for a QTL experiment

arithscan

Arithmetic operators for scanone and scantwo results

mqmaugment

MQM augmentation

nqrank

Transform a vector of quantitative values to the corresponding normal quantiles

phenames

Pull out the phenotypes names from a cross

cbind.scanoneperm

Combine columns from multiple scanone permutation results

ntyped

Number of genotypes

cbind.scantwoperm

Combine scantwo permutations by column

calc.penalties

Calculate LOD penalties

mqmplot.heatmap

Heatmap of a genome of MQM scan on multiple phenotypes

plotMissing

Plot grid of missing genotypes

mqmautocofactors

Automatic setting of cofactors, taking marker density into account

fitstahl

Fit Stahl interference model

inferFounderHap

Crude reconstruction of founder haplotypes in multi-parent RIL

mqmplot.multitrait

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

simPhyloQTL

Simulate a set of intercrosses for a single diallelic QTL

nchr

Determine the number of chromosomes

arithscanperm

Arithmetic Operators for permutation results

mqmplot.permutations

Plot results from mqmpermutation

plot.cross

Plot various features of a cross object

locateXO

Estimate locations of crossovers

bayesint

Bayesian credible interval

plotModel

Plot a QTL model

nphe

Determine the number of phenotypes QTL experiment

summary.scantwo

Summarize the results of a two-dimensional genome scan

pull.genoprob

Pull out the genotype probabilities from a cross

pull.draws

Pull out the genotype imputations from a cross

fake.4way

Simulated data for a 4-way cross

subset.map

Subsetting chromosomes for a genetic map

makeqtl

Make a qtl object

cleanGeno

Delete genotypes that are possibly in error

mqmextractmarkers

MQM marker extraction

geno.table

Create table of genotype distributions

pull.geno

Pull out the genotype data from a cross

convert.scantwo

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

addint

Add pairwise interaction to a multiple-QTL model

mqmsetcofactors

Set cofactors at fixed intervals, to be used with MQM

mqmscan

Genome scan with a multiple QTL model (MQM)

bristle3

Data on bristle number in Drosophila

jittermap

Jitter marker positions in a genetic map

addtoqtl

Add to a qtl object

replaceqtl

Replace a QTL in a qtl object with a different position

chrlen

Chromosome lengths in QTL experiment

inferredpartitions

Identify inferred partitions in mapping QTL to a phylogenetic tree

find.marker

Find marker closest to a specified position

nullmarkers

Identify markers without any genotype data

drop.dupmarkers

Drop duplicate markers

fill.geno

Fill holes in genotype data

scanPhyloQTL

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

markernames

Pull out the marker names from a cross

plotPheno

Plot a phenotype distribution

map10

An example genetic map

scanonevar.varperm

Permutation test for variance effect in scanonevar

scanonevar.meanperm

Permutation test for mean effect in scanonevar

simulatemissingdata

Simulates missing genotype data

summary.scanone

Summarize the results of a genome scans

mqmprocesspermutation

Convert mqmmulti objects into a scanoneperm object

c.cross

Combine data for QTL experiments

find.pseudomarker

Find the pseudomarker closest to a specified position

est.rf

Estimate pairwise recombination fractions

readMWril

Read data for 4- or 8-way RIL

addqtl

Scan for an additional QTL in a multiple-QTL model

mqmplot.circle

Circular genome plot for MQM

plot.qtl

Plot QTL locations

add.cim.covar

Indicate marker covariates from composite interval mapping

geno.crosstab

Create table of two-locus genotypes

replacemap.scantwo

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

subset.scantwo

Subsetting the results of a 2-d genome scan

nind

Determine the number of individuals QTL experiment

listeria

Data on Listeria monocytogenes susceptibility

flip.order

Flip the orders of markers on a set of chromosomes

calc.genoprob

Calculate conditional genotype probabilities

subset.cross

Subsetting data for QTL experiment

switch.order

Switch the order of markers on a chromosome

addpair

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

groupclusteredheatmap

Retrieving groups of traits after clustering

locations

Genetic locations of traits for the multitrait dataset

mqmscanall

Parallelized MQM on multiple phenotypes in a cross object

sim.geno

Simulate genotypes given observed marker data

addloctocross

Add phenotype location into a cross object

effectscan

Plot estimated QTL effects across the whole genome

refineqtl

Refine the positions of QTL

mqmtestnormal

Shapiro normality test used for MQM

interpPositions

Interpolate positions from one map to another

pull.markers

Drop all but a selected set of markers

find.markerpos

Find position of a marker

mqmpermutation

Estimate QTL LOD score significance using permutations or simulations

reduce2grid

Reduce to a grid of pseudomarkers.

pull.map

Pull out the genetic map from a cross

pull.rf

Pull out recombination fractions or LOD scores from a cross object

scantwo

Two-dimensional genome scan with a two-QTL model

pickMarkerSubset

Identify the largest subset of markers that are some distance apart

reorderqtl

Reorder the QTL in a qtl object

orderMarkers

Find an initial order for markers within chromosomes

summary.cross

Print summary of QTL experiment

summary.qtl

Print summary of a QTL object

comparegeno

Compare individuals' genotype data

bristleX

Data on bristle number in Drosophila

subset.scanoneperm

Subsetting permutation test results

allchrsplits

Test all possible splits of a chromosome into two pieces

tryallpositions

Test all possible positions for a marker

replace.map

Replace the genetic map of a cross

subset.scantwoperm

Subsetting two-dimensional permutation test results

simFounderSnps

Simulate founder SNPs for a multiple-strain RIL

strip.partials

Strip partially informative genotypes

convert.map

Change map function for a genetic map

droponemarker

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

sim.cross

Simulate a QTL experiment

plot.scantwo

Plot LOD scores for a two-dimensional genome scan

summary.fitqtl

Summary of fit of qtl model

c.scanone

Combine columns from multiple scanone results

mqmplot.cistrans

cis-trans plot

c.scantwoperm

Combine data from scantwo permutations

countXO

Count number of obligate crossovers for each individual

stepwiseqtl

Stepwise selection for multiple QTL

rescalemap

Rescale genetic maps

find.flanking

Find flanking markers for a specified position

movemarker

Move a marker to a new chromosome

switchAlleles

Switch alleles at selected markers

nqtl

Determine the number of QTL in a QTL object

mqmplot.directedqtl

Plot LOD*Effect curves of a multiple-QTL model

subset.scanone

Subsetting the results of a genome scan

nmissing

Number of missing genotypes

plotPXG

Plot phenotypes versus marker genotypes

plot.scanPhyloQTL

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

shiftmap

Shift starting points in genetic maps

plot.rfmatrix

Plot recombination fractions or LOD scores for a single marker

summary.scantwoperm

LOD thresholds from scantwo permutation results

summaryMap

Print summary of a genetic map

scantwopermhk

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

sim.map

Simulate a genetic map

plotMap

Plot genetic map

mqmgetmodel

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

mqmplot.cofactors

Plot cofactors on the genetic map

plotGeno

Plot observed genotypes, flagging likely errors

plotLodProfile

Plot 1-d LOD profiles for a multiple QTL model

plot.scanoneperm

Plot permutation results for a single-QTL genome scan

pull.argmaxgeno

Pull out the results of the Viterbi algorithm from a cross

plot.scantwoperm

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

scanoneboot

Bootstrap to get interval estimate of QTL location

summary.ripple

Print summary of ripple results

summary.scanoneperm

LOD thresholds from scanone permutation results

summary.scanPhyloQTL

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

xaxisloc.scanone

Get x-axis locations in scanone plot

typingGap

Maximum distance between genotyped markers