Tools for Analyzing QTL Experiments
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Documentation for package ‘qtl’ version 1.60
Help Pages
A B C D E F G H I J L M N O P Q R S T W X misc
| qtl-package | Introductory comments on R/qtl |
-- A --
| 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 |
-- B --
| 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 --
| 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.scanone | Combine columns from multiple scanone results |
| cbind.scanoneperm | Combine columns from multiple scanone permutation results |
| cbind.scantwo | Combine columns from multiple scantwo 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 |
-- D --
| 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 |
-- E --
| 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 |
-- F --
| 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 |
-- G --
| 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 |
-- H --
| hyper | Data on hypertension |
-- I --
| 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 |
-- J --
| jittermap | Jitter marker positions in a genetic map |
-- L --
| listeria | Data on Listeria monocytogenes susceptibility |
| locateXO | Estimate locations of crossovers |
| locations | Genetic locations of traits for the multitrait dataset |
| lodint | LOD support interval |
-- M --
| 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.scanone | Maximum peak in genome scan |
| max.scanPhyloQTL | Maximum peak in genome scan to map a QTL to a phylogenetic tree |
| max.scantwo | Maximum peak in two-dimensional genome scan |
| movemarker | Move a marker to a new chromosome |
| MQM | Introduction to Multiple QTL Model (MQM) mapping |
| 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 |
-- N --
| 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 |
-- O --
| orderMarkers | Find an initial order for markers within chromosomes |
-- P --
| 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.map | Plot genetic map |
| plot.qtl | Plot QTL locations |
| plot.rfmatrix | Plot recombination fractions or LOD scores for a single marker |
| 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.scanPhyloQTL | Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree |
| 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 |
| plotPheno | Plot a phenotype distribution |
| plotPXG | Plot phenotypes versus marker genotypes |
| 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 |
-- Q --
| qtlversion | Installed version of R/qtl |
-- R --
| rbind.scanoneperm | Combine data from scanone permutations |
| rbind.scantwoperm | Combine data from scantwo permutations |
| 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.cross | 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 |
-- S --
| 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 |
| scanPhyloQTL | Single-QTL genome scan to map QTL to a phylogenetic tree |
| 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.map | Print summary of a genetic map |
| summary.qtl | Print summary of a QTL object |
| summary.ripple | Print summary of ripple results |
| 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.scanPhyloQTL | Summarize the results a genome scan to map a QTL to a phylogenetic tree |
| 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 |
-- T --
| 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 |
-- W --
| write.cross | Write data for a QTL experiment to a file |
-- X --
| xaxisloc.scanone | Get x-axis locations in scanone plot |
-- misc --
| +.scanone | Arithmetic operators for scanone and scantwo results |
| +.scanoneperm | Arithmetic Operators for permutation results |
| +.scantwo | Arithmetic operators for scanone and scantwo results |
| +.scantwoperm | Arithmetic Operators for permutation results |
| -.scanone | Arithmetic operators for scanone and scantwo results |
| -.scanoneperm | Arithmetic Operators for permutation results |
| -.scantwo | Arithmetic operators for scanone and scantwo results |
| -.scantwoperm | Arithmetic Operators for permutation results |
| [.cross | Subsetting data for QTL experiment |
| [.map | Subsetting chromosomes for a genetic map |
| [.scanoneperm | Subsetting permutation test results |
| [.scantwoperm | Subsetting two-dimensional permutation test results |