EVOLUTION-MANAGER

Edit File: INDEX

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