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qtl (version 1.13-7)

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

5,612

Version

1.13-7

License

GPL-3

Maintainer

Karl W Broman

Last Published

September 10th, 2009

Functions in qtl (1.13-7)

clean.cross

Remove derived data

c.scanone

Combine columns from multiple scanone results

chrlen

Chromosome lengths in QTL experiment

addint

Add pairwise interaction to a multiple-QTL model

convert2sa

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

plotModel

Plot a QTL model

chrnames

Pull out the chromosome names from a cross

arithscanperm

Arithmetic Operators for permutation results

add.threshold

Add significance threshold to plot

comparecrosses

Compare two cross objects.

listeria

Data on Listeria monocytogenes susceptibility

formLinkageGroups

Partition markers into linkage groups

c.cross

Combine data for QTL experiments

nmar

Determine the numbers of markers on each chromosome

summary.cross

Print summary of QTL experiment

summary.fitqtl

Summary of fit of qtl model

fitstahl

Fit Stahl interference model

c.scantwo

Combine columns from multiple scantwo results

nmissing

Number of missing genotypes

calc.errorlod

Identify likely genotyping errors

arithscan

Arithmetic operators for scanone and scantwo results

cim

Composite interval mapping

replacemap.scantwo

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

tryallpositions

Test all possible positions for a marker

replace.map

Replace the genetic map of a cross

bayesint

Bayesian credible interval

qtlversion

Installed version of R/qtl

replacemap.scanone

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

calc.penalties

Calculate LOD penalties

findDupMarkers

Find markers with identical genotype data

summary.scantwo.old

Summarize the results of a two-dimensional genome scan

find.marker

Find marker closest to a specified position

clean.scantwo

Clean up scantwo output

map10

An example genetic map

geno.crosstab

Create table of two-locus genotypes

plot.geno

Plot observed genotypes, flagging likely errors

compareorder

Compare two orderings of markers on a chromosome

plot.pheno

Plot a phenotype distribution

bristle3

Data on bristle number in Drosophila

movemarker

Move a marker to a new chromosome

badorder

An intercross with misplaced markers

find.pseudomarker

Find the pseudomarker closest to a specified position

jittermap

Jitter marker positions in a genetic map

plot.scanone

Plot LOD curves

find.markerpos

Find position of a marker.

plot.scantwoperm

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

convert.scantwo

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

argmax.geno

Reconstruct underlying genotypes

nind

Determine the number of individuals QTL experiment

drop.nullmarkers

Drop markers without any genotype data

c.scantwoperm

Combine data from scantwo permutations

countXO

Count number of obligate crossovers for each individual

addtoqtl

Add to a qtl object

bristleX

Data on bristle number in Drosophila

plot.scanoneboot

Plot results of bootstrap for QTL position.

comparegeno

Compare individuals' genotype data

est.map

Estimate genetic maps

add.cim.covar

Indicate marker covariates from composite interval mapping

checkAlleles

Identify markers with switched alleles

c.scanoneperm

Combine data from scanone permutations

locateXO

Estimate locations of crossovers

fake.f2

Simulated data for an F2 intercross

geno.image

Plot grid of genotype data

summary.scantwoperm

LOD thresholds from scantwo permutation results

refineqtl

Refine the positions of QTL

plotLodProfile

Plot 1-d LOD profiles for a multiple QTL model

subset.map

Subsetting chromosomes for a genetic map

est.rf

Estimate pairwise recombination fractions

addcovarint

Add QTL x covariate interaction to a multiple-QTL model

pull.geno

Pull out the genotype data from a cross

calc.genoprob

Calculate conditional genotype probabilities

drop.markers

Drop a set of markers

pull.map

Pull out the genetic map from a cross

cbind.scanoneperm

Combine columns from multiple scanone permutation results

replaceqtl

Replace a QTL in a qtl object with a different position.

fitqtl

Fit a multiple-QTL model

condense.scantwo

Condense the output from a 2-d genome scan

effectscan

Plot estimated QTL effects across the whole genome

sim.cross

Simulate a QTL experiment

nphe

Determine the number of phenotypes QTL experiment

scanoneboot

Bootstrap to get interval estimate of QTL location

plot.missing

Plot grid of missing genotypes

pull.pheno

Pull out phenotype data from a cross

reorderqtl

Reorder the QTL in a qtl object.

plot.map

Plot genetic map

dropfromqtl

Drop a QTL from a qtl object

summary.qtl

Print summary of a QTL object

simFounderSnps

Simulate founder SNPs for a multiple-strain RIL

ripple

Compare marker orders

fill.geno

Fill holes in genotype data

top.errorlod

List genotypes with large error LOD scores

geno.table

Create table of genotype distributions

fake.4way

Simulated data for a 4-way cross

readMWril

Read data for 4- or 8-way RIL

ntyped

Number of genotypes

read.cross

Read data for a QTL experiment

summary.map

Print summary of a genetic map

subset.cross

Subsetting data for QTL experiment

stepwiseqtl

Stepwise selection for multiple QTL

summary.scanone

Summarize the results of a genome scans

makeqtl

Make a qtl object

plot.scanoneperm

Plot permutation results for a single-QTL genome scan

find.pheno

Find column number for a particular phenotype.

sim.geno

Simulate genotypes given observed marker data

summary.scanoneperm

LOD thresholds from scanone permutation results

write.cross

Write data for a QTL experiment to a file

xaxisloc.scanone

Get x-axis locations in scanone plot.

scantwo

Two-dimensional genome scan with a two-QTL model

summary.scantwo

Summarize the results of a two-dimensional genome scan

addpair

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

switch.order

Switch the order of markers on a chromosome

scanone

Genome scan with a single QTL model

subset.scantwoperm

Subsetting two-dimensional permutation test results

A starting point

Introductory comments on R/qtl

effectplot

Plot phenotype means against genotypes at one or two markers.

totmar

Determine the total number of markers

plot.pxg

Plot phenotypes versus marker genotypes.

lodint

LOD support interval

summary.scanoneboot

Bootstrap confidence interval for QTL location

find.flanking

Find flanking markers for a specified position

orderMarkers

Find an initial order for markers within chromosomes

markernames

Pull out the marker names from a cross

Print summary of ripple results

max.scantwo

Maximum peak in two-dimensional genome scan

plot.cross

Plot various features of a cross object

subset.scanone

Subsetting the results of a genome scan

convert.scanone

Convert output from scanone for R/qtl version 0.98

plot.rf

Plot recombination fractions

scanqtl

General QTL scan

qtl-internal

Internal qtl functions

plot.errorlod

Plot grid of error LOD values

subset.scanoneperm

Subsetting permutation test results

nchr

Determine the number of chromosomes

addqtl

Scan for an additional QTL in a multiple-QTL model

subset.scantwo

Subsetting the results of a 2-d genome scan

sim.map

Simulate a genetic map

fake.bc

Simulated data for a backcross

max.scanone

Maximum peak in genome scan

strip.partials

Strip partially informative genotypes

plot.scantwo

Plot LOD scores for a two-dimensional genome scan

plot.info

Plot the proportion of missing genotype information