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qtl (version 1.42-8)

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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install.packages('qtl')

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3,520

Version

1.42-8

License

GPL-3

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Repository

https://github.com/kbroman/qtl

Homepage

https://rqtl.org

Maintainer

Karl W Broman

Last Published

February 19th, 2018

Functions in qtl (1.42-8)

add.cim.covar

Indicate marker covariates from composite interval mapping

addloctocross

Add phenotype location into a cross object

addmarker

Add a marker to a cross

bristle3

Data on bristle number in Drosophila

arithscanperm

Arithmetic Operators for permutation results

calc.penalties

Calculate LOD penalties

c.cross

Combine data for QTL experiments

c.scantwo

Combine columns from multiple scantwo results

c.scantwoperm

Combine data from scantwo permutations

badorder

An intercross with misplaced markers

comparecrosses

Compare two cross objects

comparegeno

Compare individuals' genotype data

calc.errorlod

Identify likely genotyping errors

cbind.scanoneperm

Combine columns from multiple scanone permutation results

MQM

Introduction to Multiple QTL Model (MQM) mapping

drop.markers

Drop a set of markers

condense.scantwo

Condense the output from a 2-d genome scan

compareorder

Compare two orderings of markers on a chromosome

calc.genoprob

Calculate conditional genotype probabilities

convert.map

Change map function for a genetic map

chrlen

Chromosome lengths in QTL experiment

drop.nullmarkers

Drop markers without any genotype data

chrnames

Pull out the chromosome names from a cross

convert.scanone

Convert output from scanone for R/qtl version 0.98

A starting point

Introductory comments on R/qtl

effectplot

Plot phenotype means against genotypes at one or two markers

fake.f2

Simulated data for an F2 intercross

addtoqtl

Add to a qtl object

allchrsplits

Test all possible splits of a chromosome into two pieces

c.scanone

Combine columns from multiple scanone results

cleanGeno

Delete genotypes that are possibly in error

countXO

Count number of obligate crossovers for each individual

c.scanoneperm

Combine data from scanone permutations

drop.dupmarkers

Drop duplicate markers

clean.scantwo

Clean up scantwo output

find.flanking

Find flanking markers for a specified position

fill.geno

Fill holes in genotype data

effectscan

Plot estimated QTL effects across the whole genome

find.marker

Find marker closest to a specified position

addpair

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

geno.table

Create table of genotype distributions

find.pseudomarker

Find the pseudomarker closest to a specified position

convert.scantwo

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

findDupMarkers

Find markers with identical genotype data

est.map

Estimate genetic maps

getid

Pull out the individual identifiers from a cross

addqtl

Scan for an additional QTL in a multiple-QTL model

est.rf

Estimate pairwise recombination fractions

find.markerindex

Determine the numeric index for a marker

inferFounderHap

Crude reconstruction of founder haplotypes in multi-parent RIL

inferredpartitions

Identify inferred partitions in mapping QTL to a phylogenetic tree

argmax.geno

Reconstruct underlying genotypes

map2table

Convert genetic map from list to table.

An example genetic map

fitqtl

Fit a multiple-QTL model

mqmautocofactors

Automatic setting of cofactors, taking marker density into account

groupclusteredheatmap

Retrieving groups of traits after clustering

locations

Genetic locations of traits for the multitrait dataset

arithscan

Arithmetic operators for scanone and scantwo results

hyper

Data on hypertension

convert2riself

Convert a cross to RIL by selfing

mapthis

Simulated data for illustrating genetic map construction

dropfromqtl

Drop a QTL from a qtl object

mqmplot.clusteredheatmap

Plot clustered heatmap of MQM scan on multiple phenotypes

droponemarker

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

mqmextractmarkers

MQM marker extraction

mqmplot.cofactors

Plot cofactors on the genetic map

lodint

LOD support interval

mqmgetmodel

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

mqmfind.marker

Fetch significant markers after permutation analysis

movemarker

Move a marker to a new chromosome

max.scantwo

Maximum peak in two-dimensional genome scan

find.markerpos

Find position of a marker

mqmpermutation

Estimate QTL LOD score significance using permutations or simulations

mqmplot.directedqtl

Plot LOD*Effect curves of a multiple-QTL model

cbind.scantwoperm

Combine scantwo permutations by column

find.pheno

Find column number for a particular phenotype

checkAlleles

Identify markers with switched alleles

mqmplot.heatmap

Heatmap of a genome of MQM scan on multiple phenotypes

cim

Composite interval mapping

nmar

Determine the numbers of markers on each chromosome

mqmprocesspermutation

Convert mqmmulti objects into a scanoneperm object

mqmplot.singletrait

Plot LOD curves of a multiple-QTL model

mqmscanfdr

Estimate FDR for multiple trait QTL analysis

clean.cross

Remove derived data

phenames

Pull out the phenotypes names from a cross

mqmsetcofactors

Set cofactors at fixed intervals, to be used with MQM

convert2risib

Convert a cross to RIL by sib mating

geno.image

Plot grid of genotype data

geno.crosstab

Create table of two-locus genotypes

nmissing

Number of missing genotypes

interpPositions

Interpolate positions from one map to another

fake.4way

Simulated data for a 4-way cross

multitrait

Example Cross object from R/QTL with multiple traits

convert2sa

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

mqmtestnormal

Shapiro normality test used for MQM

nqtl

Determine the number of QTL in a QTL object

jittermap

Jitter marker positions in a genetic map

pickMarkerSubset

Identify the largest subset of markers that are some distance apart

markerlrt

General likelihood ratio test for association between marker pairs

ntyped

Number of genotypes

markernames

Pull out the marker names from a cross

fake.bc

Simulated data for a backcross

fitstahl

Fit Stahl interference model

mqmplot.multitrait

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

mqmplot.permutations

Plot results from mqmpermutation

flip.order

Flip the orders of markers on a set of chromosomes

mqmscan

Genome scan with a multiple QTL model (MQM)

formMarkerCovar

Create matrix of marker covariates for QTL analysis

listeria

Data on Listeria monocytogenes susceptibility

formLinkageGroups

Partition markers into linkage groups

mqmscanall

Parallelized MQM on multiple phenotypes in a cross object

max.scanPhyloQTL

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

nphe

Determine the number of phenotypes QTL experiment

plotMap

Plot genetic map

locateXO

Estimate locations of crossovers

nqrank

Transform a vector of quantitative values to the corresponding normal quantiles

plot.cross

Plot various features of a cross object

plotErrorlod

Plot grid of error LOD values

plotMissing

Plot grid of missing genotypes

plot.scanone

Plot LOD curves

plot.scanoneboot

Plot results of bootstrap for QTL position

plotGeno

Plot observed genotypes, flagging likely errors

plotPheno

Plot a phenotype distribution

plotInfo

Plot the proportion of missing genotype information

max.scanone

Maximum peak in genome scan

plotPXG

Plot phenotypes versus marker genotypes

pull.rf

Pull out recombination fractions or LOD scores from a cross object

plot.rfmatrix

Plot recombination fractions or LOD scores for a single marker

qtl-internal

Internal qtl functions

plot.scanPhyloQTL

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

mqmplot.circle

Circular genome plot for MQM

pull.map

Pull out the genetic map from a cross

pull.genoprob

Pull out the genotype probabilities from a cross

refineqtl

Refine the positions of QTL

mqmplot.cistrans

cis-trans plot

nchr

Determine the number of chromosomes

replacemap.scantwo

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

replaceqtl

Replace a QTL in a qtl object with a different position

plotModel

Plot a QTL model

scanoneboot

Bootstrap to get interval estimate of QTL location

plot.scanoneperm

Plot permutation results for a single-QTL genome scan

reorderqtl

Reorder the QTL in a qtl object

scanqtl

General QTL scan

scanonevar

Genome scan for QTL affecting mean and/or variance

pull.argmaxgeno

Pull out the results of the Viterbi algorithm from a cross

nind

Determine the number of individuals QTL experiment

qtlversion

Installed version of R/qtl

scantwo

Two-dimensional genome scan with a two-QTL model

subset.cross

Subsetting data for QTL experiment

read.cross

Read data for a QTL experiment

plot.scantwo

Plot LOD scores for a two-dimensional genome scan

nullmarkers

Identify markers without any genotype data

subset.map

Subsetting chromosomes for a genetic map

orderMarkers

Find an initial order for markers within chromosomes

summary.ripple

Print summary of ripple results

rescalemap

Rescale genetic maps

strip.partials

Strip partially informative genotypes

stepwiseqtl

Stepwise selection for multiple QTL

ripple

Compare marker orders

summary.scanPhyloQTL

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

pull.markers

Drop all but a selected set of markers

summaryMap

Print summary of a genetic map

pull.pheno

Pull out phenotype data from a cross

replace.map

Replace the genetic map of a cross

plot.qtl

Plot QTL locations

scanPhyloQTL

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

switch.order

Switch the order of markers on a chromosome

replacemap.scanone

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

plotRF

Plot recombination fractions

scantwopermhk

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

switchAlleles

Switch alleles at selected markers

summary.qtl

Print summary of a QTL object

simPhyloQTL

Simulate a set of intercrosses for a single diallelic QTL

scanone

Genome scan with a single QTL model

simulatemissingdata

Simulates missing genotype data

shiftmap

Shift starting points in genetic maps

subset.scanone

Subsetting the results of a genome scan

write.cross

Write data for a QTL experiment to a file

summaryScantwoOld

Summarize the results of a two-dimensional genome scan

xaxisloc.scanone

Get x-axis locations in scanone plot

summary.scantwoperm

LOD thresholds from scantwo permutation results

subset.scanoneperm

Subsetting permutation test results

plot.scantwoperm

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

plotLodProfile

Plot 1-d LOD profiles for a multiple QTL model

table2map

Convert a table of marker positions to a map object.

pull.draws

Pull out the genotype imputations from a cross

top.errorlod

List genotypes with large error LOD scores

pull.geno

Pull out the genotype data from a cross

sim.map

Simulate a genetic map

readMWril

Read data for 4- or 8-way RIL

totmar

Determine the total number of markers

reduce2grid

Reduce to a grid of pseudomarkers.

transformPheno

Transformation of the phenotypes in a cross object

scanonevar.meanperm

Permutation test for mean effect in scanonevar

scanonevar.varperm

Permutation test for variance effect in scanonevar

simFounderSnps

Simulate founder SNPs for a multiple-strain RIL

sim.cross

Simulate a QTL experiment

summary.cross

Print summary of QTL experiment

summary.scanoneperm

LOD thresholds from scanone permutation results

summary.fitqtl

Summary of fit of qtl model

summary.scantwo

Summarize the results of a two-dimensional genome scan

sim.geno

Simulate genotypes given observed marker data

tryallpositions

Test all possible positions for a marker

subset.scantwo

Subsetting the results of a 2-d genome scan

subset.scantwoperm

Subsetting two-dimensional permutation test results

summary.scanone

Summarize the results of a genome scans

typingGap

Maximum distance between genotyped markers

summary.scanoneboot

Bootstrap confidence interval for QTL location

addcovarint

Add QTL x covariate interaction to a multiple-QTL model

addint

Add pairwise interaction to a multiple-QTL model

add.threshold

Add significance threshold to plot

bristleX

Data on bristle number in Drosophila

bayesint

Bayesian credible interval