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A B C D E F G H J L M N O P Q R S T W X misc
| qtl-package | Introductory comments on R/qtl |
| +.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 |
| 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 |
| 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 |
| 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.scanone | Combine columns from multiple scanone results |
| cbind.scanoneperm | Combine columns from multiple scanone permutation results |
| cbind.scantwo | Combine columns from multiple scantwo results |
| 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 |
| 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.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 |
| convert2sa | Convert a sex-specific map to a sex-averaged one. |
| countXO | Count number of obligate crossovers for each individual |
| drop.markers | Drop a set of markers |
| drop.nullmarkers | Drop markers without any genotype data |
| dropfromqtl | Drop a QTL from a qtl object |
| 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.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 |
| fitqtl | Fit a multiple-QTL model |
| fitstahl | Fit Stahl interference model |
| formLinkageGroups | Partition markers into linkage groups |
| geno.crosstab | Create table of two-locus genotypes |
| geno.image | Plot grid of genotype data |
| geno.table | Create table of genotype distributions |
| hyper | Data on hypertension |
| jittermap | Jitter marker positions in a genetic map |
| listeria | Data on Listeria monocytogenes susceptibility |
| locateXO | Estimate locations of crossovers |
| lodint | LOD support interval |
| makeqtl | Make a qtl object |
| map10 | An example genetic map |
| markernames | Pull out the marker names from a cross |
| max.scanone | Maximum peak in genome scan |
| max.scantwo | Maximum peak in two-dimensional genome scan |
| movemarker | Move a marker to a new chromosome |
| 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 |
| ntyped | Number of genotypes |
| orderMarkers | Find an initial order for markers within chromosomes |
| plot.cross | Plot various features of a cross object |
| plot.errorlod | Plot grid of error LOD values |
| plot.geno | Plot observed genotypes, flagging likely errors |
| plot.info | Plot the proportion of missing genotype information |
| plot.map | Plot genetic map |
| plot.missing | Plot grid of missing genotypes |
| plot.pheno | Plot a phenotype distribution |
| plot.pxg | Plot phenotypes versus marker genotypes. |
| plot.qtl | Plot QTL locations |
| plot.rf | Plot recombination fractions |
| 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 |
| plotLodProfile | Plot 1-d LOD profiles for a multiple QTL model |
| plotModel | Plot a QTL model |
| pull.geno | Pull out the genotype data from a cross |
| pull.map | Pull out the genetic map from a cross |
| pull.pheno | Pull out phenotype data from a cross |
| qtlversion | Installed version of R/qtl |
| 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 |
| 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. |
| ripple | Compare marker orders |
| scanone | Genome scan with a single QTL model |
| scanoneboot | Bootstrap to get interval estimate of QTL location |
| scanqtl | General QTL scan |
| scantwo | Two-dimensional genome scan with a two-QTL model |
| 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 |
| 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.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.scantwo | Summarize the results of a two-dimensional genome scan |
| summary.scantwo.old | Summarize the results of a two-dimensional genome scan |
| summary.scantwoperm | LOD thresholds from scantwo permutation results |
| switch.order | Switch the order of markers on a chromosome |
| top.errorlod | List genotypes with large error LOD scores |
| totmar | Determine the total number of markers |
| tryallpositions | Test all possible positions for a marker |
| write.cross | Write data for a QTL experiment to a file |
| xaxisloc.scanone | Get x-axis locations in scanone plot. |
| [.cross | Subsetting data for QTL experiment |
| [.map | Subsetting chromosomes for a genetic map |