Introductory comments on R/qtl | qtl-package |
Indicate marker covariates from composite interval mapping | add.cim.covar |
Add significance threshold to plot | add.threshold |
Add QTL x covariate interaction to a multiple-QTL model | addcovarint |
Add pairwise interaction to a multiple-QTL model | addint |
Add phenotype location into a cross object | addloctocross |
Add a marker to a cross | addmarker |
Scan for an additional pair of QTL in a multiple-QTL model | addpair |
Scan for an additional QTL in a multiple-QTL model | addqtl |
Add to a qtl object | addtoqtl |
Test all possible splits of a chromosome into two pieces | allchrsplits |
Reconstruct underlying genotypes | argmax.geno |
Arithmetic operators for scanone and scantwo results | +.scanone +.scantwo -.scanone -.scantwo |
Arithmetic Operators for permutation results | +.scanoneperm +.scantwoperm -.scanoneperm -.scantwoperm |
An intercross with misplaced markers | badorder |
Bayesian credible interval | bayesint |
Data on bristle number in Drosophila | bristle3 |
Data on bristle number in Drosophila | bristleX |
Combine data for QTL experiments | c.cross |
Combine columns from multiple scanone results | c.scanone cbind.scanone |
Combine data from scanone permutations | c.scanoneperm rbind.scanoneperm |
Combine columns from multiple scantwo results | c.scantwo cbind.scantwo |
Combine data from scantwo permutations | c.scantwoperm rbind.scantwoperm |
Identify likely genotyping errors | calc.errorlod |
Calculate conditional genotype probabilities | calc.genoprob |
Calculate LOD penalties | calc.penalties |
Combine columns from multiple scanone permutation results | cbind.scanoneperm |
Combine scantwo permutations by column | cbind.scantwoperm |
Identify markers with switched alleles | checkAlleles |
Chromosome lengths in QTL experiment | chrlen |
Pull out the chromosome names from a cross | chrnames |
Composite interval mapping | cim |
Remove derived data | clean.cross |
Clean up scantwo output | clean.scantwo |
Delete genotypes that are possibly in error | cleanGeno |
Compare two cross objects | comparecrosses |
Compare individuals' genotype data | comparegeno |
Compare two orderings of markers on a chromosome | compareorder |
Condense the output from a 2-d genome scan | condense.scantwo |
Change map function for a genetic map | convert.map |
Convert output from scanone for R/qtl version 0.98 | convert.scanone |
Convert output from scantwo for R/qtl version 1.03 and earlier | convert.scantwo |
Convert a cross to RIL by selfing | convert2riself |
Convert a cross to RIL by sib mating | convert2risib |
Convert a sex-specific map to a sex-averaged one | convert2sa |
Count number of obligate crossovers for each individual | countXO |
Drop duplicate markers | drop.dupmarkers |
Drop a set of markers | drop.markers |
Drop markers without any genotype data | drop.nullmarkers |
Drop a QTL from a qtl object | dropfromqtl |
Drop one marker at a time and determine effect on genetic map | droponemarker |
Plot phenotype means against genotypes at one or two markers | effectplot |
Plot estimated QTL effects across the whole genome | effectscan |
Estimate genetic maps | est.map |
Estimate pairwise recombination fractions | est.rf |
Simulated data for a 4-way cross | fake.4way |
Simulated data for a backcross | fake.bc |
Simulated data for an F2 intercross | fake.f2 |
Fill holes in genotype data | fill.geno |
Find large intervals in a map | find_large_intervals |
Find flanking markers for a specified position | find.flanking |
Find marker closest to a specified position | find.marker |
Determine the numeric index for a marker | find.markerindex |
Find position of a marker | find.markerpos |
Find column number for a particular phenotype | find.pheno |
Find the pseudomarker closest to a specified position | find.pseudomarker |
Find markers with identical genotype data | findDupMarkers |
Fit a multiple-QTL model | fitqtl |
Fit Stahl interference model | fitstahl |
Flip the orders of markers on a set of chromosomes | flip.order |
Partition markers into linkage groups | formLinkageGroups |
Create matrix of marker covariates for QTL analysis | formMarkerCovar |
Create table of two-locus genotypes | geno.crosstab |
Plot grid of genotype data | geno.image |
Create table of genotype distributions | geno.table |
Pull out the individual identifiers from a cross | getid |
Retrieving groups of traits after clustering | groupclusteredheatmap |
Data on hypertension | hyper |
Crude reconstruction of founder haplotypes in multi-parent RIL | inferFounderHap |
Identify inferred partitions in mapping QTL to a phylogenetic tree | inferredpartitions |
Interpolate positions from one map to another | interpPositions |
Jitter marker positions in a genetic map | jittermap |
Data on Listeria monocytogenes susceptibility | listeria |
Estimate locations of crossovers | locateXO |
Genetic locations of traits for the multitrait dataset | locations |
LOD support interval | lodint |
Make a qtl object | makeqtl |
An example genetic map | map10 |
Convert genetic map from list to table. | map2table |
Simulated data for illustrating genetic map construction | mapthis |
General likelihood ratio test for association between marker pairs | markerlrt |
Pull out the marker names from a cross | markernames |
Maximum peak in genome scan | max.scanone |
Maximum peak in genome scan to map a QTL to a phylogenetic tree | max.scanPhyloQTL |
Maximum peak in two-dimensional genome scan | max.scantwo |
Move a marker to a new chromosome | movemarker |
Introduction to Multiple QTL Model (MQM) mapping | MQM |
MQM augmentation | mqmaugment |
Automatic setting of cofactors, taking marker density into account | mqmautocofactors |
MQM marker extraction | mqmextractmarkers |
Fetch significant markers after permutation analysis | mqmfind.marker |
Retrieve the QTL model used in mapping from the results of an MQM scan | mqmgetmodel |
Estimate QTL LOD score significance using permutations or simulations | mqmpermutation |
Circular genome plot for MQM | mqmplot.circle |
cis-trans plot | mqmplot.cistrans |
Plot clustered heatmap of MQM scan on multiple phenotypes | mqmplot.clusteredheatmap |
Plot cofactors on the genetic map | mqmplot.cofactors |
Plot LOD*Effect curves of a multiple-QTL model | mqmplot.directedqtl |
Heatmap of a genome of MQM scan on multiple phenotypes | mqmplot.heatmap |
Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes | mqmplot.multitrait |
Plot results from mqmpermutation | mqmplot.permutations |
Plot LOD curves of a multiple-QTL model | mqmplot.singletrait |
Convert mqmmulti objects into a scanoneperm object | mqmprocesspermutation |
Genome scan with a multiple QTL model (MQM) | mqmscan |
Parallelized MQM on multiple phenotypes in a cross object | mqmscanall |
Estimate FDR for multiple trait QTL analysis | mqmscanfdr |
Set cofactors at fixed intervals, to be used with MQM | mqmsetcofactors |
Shapiro normality test used for MQM | mqmtestnormal |
Example Cross object from R/QTL with multiple traits | multitrait |
Determine the number of chromosomes | nchr |
Determine the number of individuals QTL experiment | nind |
Determine the numbers of markers on each chromosome | nmar |
Number of missing genotypes | nmissing |
Determine the number of phenotypes QTL experiment | nphe |
Transform a vector of quantitative values to the corresponding normal quantiles | nqrank |
Determine the number of QTL in a QTL object | nqtl |
Number of genotypes | ntyped |
Identify markers without any genotype data | nullmarkers |
Find an initial order for markers within chromosomes | orderMarkers |
Pull out the phenotypes names from a cross | phenames |
Identify the largest subset of markers that are some distance apart | pickMarkerSubset |
Plot genotype comparison | plot.comparegeno |
Plot various features of a cross object | plot.cross |
Plot QTL locations | plot.qtl |
Plot recombination fractions or LOD scores for a single marker | plot.rfmatrix |
Plot LOD curves | plot.scanone |
Plot results of bootstrap for QTL position | plot.scanoneboot |
Plot permutation results for a single-QTL genome scan | plot.scanoneperm |
Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree | plot.scanPhyloQTL |
Plot LOD scores for a two-dimensional genome scan | plot.scantwo |
Plot permutation results for a 2d, 2-QTL genome scan | plot.scantwoperm |
Plot grid of error LOD values | plotErrorlod |
Plot observed genotypes, flagging likely errors | plotGeno |
Plot the proportion of missing genotype information | plotInfo |
Plot 1-d LOD profiles for a multiple QTL model | plotLodProfile |
Plot genetic map | plot.map plotMap |
Plot grid of missing genotypes | plotMissing |
Plot a QTL model | plotModel |
Plot a phenotype distribution | plotPheno |
Plot phenotypes versus marker genotypes | plotPXG |
Plot recombination fractions | plotRF |
Pull out the results of the Viterbi algorithm from a cross | pull.argmaxgeno |
Pull out the genotype imputations from a cross | pull.draws |
Pull out the genotype data from a cross | pull.geno |
Pull out the genotype probabilities from a cross | pull.genoprob |
Pull out the genetic map from a cross | pull.map |
Drop all but a selected set of markers | pull.markers |
Pull out phenotype data from a cross | pull.pheno |
Pull out recombination fractions or LOD scores from a cross object | pull.rf |
Installed version of R/qtl | qtlversion |
Read data for a QTL experiment | read.cross |
Read data for 4- or 8-way RIL | readMWril |
Reduce to a grid of pseudomarkers. | reduce2grid |
Refine the positions of QTL | refineqtl |
Reorder the QTL in a qtl object | reorderqtl |
Replace the genetic map of a cross | replace.map replacemap.cross |
Replace the genetic map in QTL mapping results with an alternate map | replacemap.scanone |
Replace the genetic map in QTL mapping results with an alternate map | replacemap.scantwo |
Replace a QTL in a qtl object with a different position | replaceqtl |
Rescale genetic maps | rescalemap |
Compare marker orders | ripple |
Genome scan with a single QTL model | scanone |
Bootstrap to get interval estimate of QTL location | scanoneboot |
Genome scan for QTL affecting mean and/or variance | scanonevar |
Permutation test for mean effect in scanonevar | scanonevar.meanperm |
Permutation test for variance effect in scanonevar | scanonevar.varperm |
Single-QTL genome scan to map QTL to a phylogenetic tree | scanPhyloQTL |
General QTL scan | scanqtl |
Two-dimensional genome scan with a two-QTL model | scantwo |
Permutation test for 2d genome scan by Haley-Knott regression | scantwopermhk |
Shift starting points in genetic maps | shiftmap |
Simulate a QTL experiment | sim.cross |
Simulate genotypes given observed marker data | sim.geno |
Simulate a genetic map | sim.map |
Simulate founder SNPs for a multiple-strain RIL | simFounderSnps |
Simulate a set of intercrosses for a single diallelic QTL | simPhyloQTL |
Simulates missing genotype data | simulatemissingdata |
Stepwise selection for multiple QTL | stepwiseqtl |
Strip partially informative genotypes | strip.partials |
Subsetting data for QTL experiment | subset.cross [.cross |
Subsetting chromosomes for a genetic map | subset.map [.map |
Subsetting the results of a genome scan | subset.scanone |
Subsetting permutation test results | subset.scanoneperm [.scanoneperm |
Subsetting the results of a 2-d genome scan | subset.scantwo |
Subsetting two-dimensional permutation test results | subset.scantwoperm [.scantwoperm |
Print pairs of individuals with similar genotype data. | summary.comparegeno |
Print summary of QTL experiment | summary.cross |
Summary of fit of qtl model | summary.fitqtl |
Print summary of a QTL object | summary.qtl |
Print summary of ripple results | summary.ripple |
Summarize the results of a genome scans | summary.scanone |
Bootstrap confidence interval for QTL location | summary.scanoneboot |
LOD thresholds from scanone permutation results | summary.scanoneperm |
Summarize the results a genome scan to map a QTL to a phylogenetic tree | summary.scanPhyloQTL |
Summarize the results of a two-dimensional genome scan | summary.scantwo |
LOD thresholds from scantwo permutation results | summary.scantwoperm |
Print summary of a genetic map | summary.map summaryMap |
Summarize the results of a two-dimensional genome scan | summaryScantwoOld |
Switch the order of markers on a chromosome | switch.order |
Switch alleles at selected markers | switchAlleles |
Convert a table of marker positions to a map object. | table2map |
List genotypes with large error LOD scores | top.errorlod |
Determine the total number of markers | totmar |
Transformation of the phenotypes in a cross object | transformPheno |
Test all possible positions for a marker | tryallpositions |
Maximum distance between genotyped markers | typingGap |
Write data for a QTL experiment to a file | write.cross |
Get x-axis locations in scanone plot | xaxisloc.scanone |