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qtl (version 1.41-6)

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

3,345

Version

1.41-6

License

GPL-3

Maintainer

Karl W Broman

Last Published

June 12th, 2017

Functions in qtl (1.41-6)

addloctocross

Add phenotype location into a cross object

addmarker

Add a marker to a cross

add.cim.covar

Indicate marker covariates from composite interval mapping

add.threshold

Add significance threshold to plot

addcovarint

Add QTL x covariate interaction to a multiple-QTL model

addint

Add pairwise interaction to a multiple-QTL model

MQM

Introduction to Multiple QTL Model (MQM) mapping

A starting point

Introductory comments on R/qtl

addpair

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

addqtl

Scan for an additional QTL in a multiple-QTL model

arithscanperm

Arithmetic Operators for permutation results

badorder

An intercross with misplaced markers

c.scantwo

Combine columns from multiple scantwo results

c.scantwoperm

Combine data from scantwo permutations

argmax.geno

Reconstruct underlying genotypes

arithscan

Arithmetic operators for scanone and scantwo results

calc.errorlod

Identify likely genotyping errors

bristle3

Data on bristle number in Drosophila

calc.penalties

Calculate LOD penalties

cbind.scanoneperm

Combine columns from multiple scanone permutation results

comparecrosses

Compare two cross objects

comparegeno

Compare individuals' genotype data

convert.scantwo

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

addtoqtl

Add to a qtl object

allchrsplits

Test all possible splits of a chromosome into two pieces

convert2risib

Convert a cross to RIL by sib mating

bayesint

Bayesian credible interval

convert2riself

Convert a cross to RIL by selfing

find.pseudomarker

Find the pseudomarker closest to a specified position

findDupMarkers

Find markers with identical genotype data

bristleX

Data on bristle number in Drosophila

c.cross

Combine data for QTL experiments

c.scanone

Combine columns from multiple scanone results

inferFounderHap

Crude reconstruction of founder haplotypes in multi-parent RIL

inferredpartitions

Identify inferred partitions in mapping QTL to a phylogenetic tree

interpPositions

Interpolate positions from one map to another

jittermap

Jitter marker positions in a genetic map

convert2sa

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

effectplot

Plot phenotype means against genotypes at one or two markers

effectscan

Plot estimated QTL effects across the whole genome

calc.genoprob

Calculate conditional genotype probabilities

clean.scantwo

Clean up scantwo output

cleanGeno

Delete genotypes that are possibly in error

convert.map

Change map function for a genetic map

convert.scanone

Convert output from scanone for R/qtl version 0.98

est.map

Estimate genetic maps

est.rf

Estimate pairwise recombination fractions

find.markerindex

Determine the numeric index for a marker

find.flanking

Find flanking markers for a specified position

find.marker

Find marker closest to a specified position

geno.crosstab

Create table of two-locus genotypes

fitqtl

Fit a multiple-QTL model

groupclusteredheatmap

Retrieving groups of traits after clustering

hyper

Data on hypertension

listeria

Data on Listeria monocytogenes susceptibility

geno.image

Plot grid of genotype data

mqmplot.multitrait

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

mqmplot.permutations

Plot results from mqmpermutation

mqmtestnormal

Shapiro normality test used for MQM

markerlrt

General likelihood ratio test for association between marker pairs

markernames

Pull out the marker names from a cross

mqmplot.circle

Circular genome plot for MQM

locateXO

Estimate locations of crossovers

max.scantwo

Maximum peak in two-dimensional genome scan

movemarker

Move a marker to a new chromosome

mqmgetmodel

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

compareorder

Compare two orderings of markers on a chromosome

condense.scantwo

Condense the output from a 2-d genome scan

fake.4way

Simulated data for a 4-way cross

fake.bc

Simulated data for a backcross

mqmpermutation

Estimate QTL LOD score significance using permutations or simulations

nqtl

Determine the number of QTL in a QTL object

ntyped

Number of genotypes

plotPheno

Plot a phenotype distribution

mqmplot.cistrans

cis-trans plot

nchr

Determine the number of chromosomes

nind

Determine the number of individuals QTL experiment

multitrait

Example Cross object from R/QTL with multiple traits

plot.cross

Plot various features of a cross object

plotErrorlod

Plot grid of error LOD values

plot.scanoneperm

Plot permutation results for a single-QTL genome scan

plot.scantwo

Plot LOD scores for a two-dimensional genome scan

pull.draws

Pull out the genotype imputations from a cross

pull.geno

Pull out the genotype data from a cross

replace.map

Replace the genetic map of a cross

replacemap.scanone

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

stepwiseqtl

Stepwise selection for multiple QTL

strip.partials

Strip partially informative genotypes

subset.scanone

Subsetting the results of a genome scan

c.scanoneperm

Combine data from scanone permutations

cim

Composite interval mapping

clean.cross

Remove derived data

drop.markers

Drop a set of markers

nmar

Determine the numbers of markers on each chromosome

nmissing

Number of missing genotypes

plotGeno

Plot observed genotypes, flagging likely errors

plotInfo

Plot the proportion of missing genotype information

plotPXG

Plot phenotypes versus marker genotypes

plot.scanone

Plot LOD curves

plot.scanoneboot

Plot results of bootstrap for QTL position

pull.genoprob

Pull out the genotype probabilities from a cross

pull.map

Pull out the genetic map from a cross

readMWril

Read data for 4- or 8-way RIL

subset.scanoneperm

Subsetting permutation test results

summary.scanone

Summarize the results of a genome scans

summary.scanoneboot

Bootstrap confidence interval for QTL location

write.cross

Write data for a QTL experiment to a file

reduce2grid

Reduce to a grid of pseudomarkers.

scantwopermhk

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

shiftmap

Shift starting points in genetic maps

subset.scantwo

Subsetting the results of a 2-d genome scan

drop.nullmarkers

Drop markers without any genotype data

dropfromqtl

Drop a QTL from a qtl object

droponemarker

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

fitstahl

Fit Stahl interference model

qtlversion

Installed version of R/qtl

read.cross

Read data for a QTL experiment

replaceqtl

Replace a QTL in a qtl object with a different position

scanPhyloQTL

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

scanone

Genome scan with a single QTL model

subset.cross

Subsetting data for QTL experiment

subset.map

Subsetting chromosomes for a genetic map

replacemap.scantwo

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

subset.scantwoperm

Subsetting two-dimensional permutation test results

switch.order

Switch the order of markers on a chromosome

switchAlleles

Switch alleles at selected markers

xaxisloc.scanone

Get x-axis locations in scanone plot

summary.scanoneperm

LOD thresholds from scanone permutation results

summary.scantwo

Summarize the results of a two-dimensional genome scan

flip.order

Flip the orders of markers on a set of chromosomes

locations

Genetic locations of traits for the multitrait dataset

Automatic setting of cofactors, taking marker density into account

mqmplot.clusteredheatmap

Plot clustered heatmap of MQM scan on multiple phenotypes

mqmplot.cofactors

Plot cofactors on the genetic map

mqmplot.singletrait

Plot LOD curves of a multiple-QTL model

mqmprocesspermutation

Convert mqmmulti objects into a scanoneperm object

phenames

Pull out the phenotypes names from a cross

pickMarkerSubset

Identify the largest subset of markers that are some distance apart

plotMap

Plot genetic map

cbind.scantwoperm

Combine scantwo permutations by column

checkAlleles

Identify markers with switched alleles

chrlen

Chromosome lengths in QTL experiment

chrnames

Pull out the chromosome names from a cross

geno.table

Create table of genotype distributions

getid

Pull out the individual identifiers from a cross

map2table

Convert genetic map from list to table.

mapthis

Simulated data for illustrating genetic map construction

plotMissing

Plot grid of missing genotypes

plot.rfmatrix

Plot recombination fractions or LOD scores for a single marker

plot.scanPhyloQTL

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

rescalemap

Rescale genetic maps

ripple

Compare marker orders

scanoneboot

Bootstrap to get interval estimate of QTL location

scanonevar

Genome scan for QTL affecting mean and/or variance

sim.cross

Simulate a QTL experiment

mqmextractmarkers

MQM marker extraction

mqmfind.marker

Fetch significant markers after permutation analysis

mqmplot.directedqtl

Plot LOD*Effect curves of a multiple-QTL model

mqmplot.heatmap

Heatmap of a genome of MQM scan on multiple phenotypes

sim.geno

Simulate genotypes given observed marker data

summary.ripple

Print summary of ripple results

summary.scanPhyloQTL

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

summaryScantwoOld

Summarize the results of a two-dimensional genome scan

mqmscan

Genome scan with a multiple QTL model (MQM)

mqmscanall

Parallelized MQM on multiple phenotypes in a cross object

nullmarkers

Identify markers without any genotype data

orderMarkers

Find an initial order for markers within chromosomes

plot.scantwoperm

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

plotLodProfile

Plot 1-d LOD profiles for a multiple QTL model

pull.markers

Drop all but a selected set of markers

countXO

Count number of obligate crossovers for each individual

drop.dupmarkers

Drop duplicate markers

fake.f2

Simulated data for an F2 intercross

fill.geno

Fill holes in genotype data

find.markerpos

Find position of a marker

find.pheno

Find column number for a particular phenotype

formLinkageGroups

Partition markers into linkage groups

formMarkerCovar

Create matrix of marker covariates for QTL analysis

summary.scantwoperm

LOD thresholds from scantwo permutation results

pull.pheno

Pull out phenotype data from a cross

scanonevar.meanperm

Permutation test for mean effect in scanonevar

scanonevar.varperm

Permutation test for variance effect in scanonevar

simPhyloQTL

Simulate a set of intercrosses for a single diallelic QTL

simulatemissingdata

Simulates missing genotype data

summaryMap

Print summary of a genetic map

makeqtl

Make a qtl object

map10

An example genetic map

max.scanPhyloQTL

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

max.scanone

Maximum peak in genome scan

summary.qtl

Print summary of a QTL object

table2map

Convert a table of marker positions to a map object.

top.errorlod

List genotypes with large error LOD scores

totmar

Determine the total number of markers

transformPheno

Transformation of the phenotypes in a cross object

mqmscanfdr

Estimate FDR for multiple trait QTL analysis

mqmsetcofactors

Set cofactors at fixed intervals, to be used with MQM

nphe

Determine the number of phenotypes QTL experiment

nqrank

Transform a vector of quantitative values to the corresponding normal quantiles

plot.qtl

Plot QTL locations

plotRF

Plot recombination fractions

plotModel

Plot a QTL model

pull.argmaxgeno

Pull out the results of the Viterbi algorithm from a cross

pull.rf

Pull out recombination fractions or LOD scores from a cross object

qtl-internal

Internal qtl functions

refineqtl

Refine the positions of QTL

reorderqtl

Reorder the QTL in a qtl object

scanqtl

General QTL scan

scantwo

Two-dimensional genome scan with a two-QTL model

sim.map

Simulate a genetic map

simFounderSnps

Simulate founder SNPs for a multiple-strain RIL

summary.cross

Print summary of QTL experiment

summary.fitqtl

Summary of fit of qtl model

typingGap

Maximum distance between genotyped markers

tryallpositions

Test all possible positions for a marker