![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Package List]](../../../doc/html/left.jpg){kind=small}
![[Top]](../../../doc/html/up.jpg){kind=small}
A B C D E F G H L M N P R S T W
| A starting point | Introductory comments |
| argmax.geno | Reconstruct underlying genotypes |
| badorder | An intercross with misplaced markers |
| bristle3 | Data on bristle number in Drosophila |
| bristleX | Data on bristle number in Drosophila |
| c.cross | Combine data for QTL experiments |
| calc.errorlod | Identify likely genotyping errors |
| calc.genoprob | Calculate conditional genotype probabilities |
| clean | Remove derived data |
| comparecrosses | Compare two cross objects. |
| convert.scanone | Convert output from scanone for R/qtl version 0.98 |
| convert2ss | Convert an intercross into a form to allow sex-specific maps |
| drop.markers | Drop a set of markers |
| drop.nullmarkers | Drop markers without any genotype data |
| effectplot | Plot phenotype means against genotypes at one or two markers. |
| effectscan | Plot allelic effect across the whole genome |
| ensembl.map | Retrieve physical map from EnsEMBL for a cross |
| 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.pheno | Find column number for a particular phenotype. |
| fitqtl | Fit a multiple QTL model |
| geno.table | Create table of genotype distributions |
| hyper | Data on hypertension |
| listeria | Data on Listeria monocytogenes susceptibility |
| lodint | LOD support interval |
| makeqtl | Make a qtl object |
| map10 | An example genetic map |
| 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 | Print summary of QTL experiment |
| nind | Print summary of QTL experiment |
| nmar | Print summary of QTL experiment |
| nmissing | Number of missing genotypes |
| nphe | Print summary of QTL experiment |
| 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.pxg | Plot phenotypes versus marker genotypes. |
| plot.rf | Plot recombination fractions |
| plot.scanone | Plot LOD curves |
| plot.scantwo | Plot LOD scores for a two-dimensional genome scan |
| print.cross | Print a QTL experiment |
| pull.geno | Pull out the genotype data from a cross |
| pull.map | Pull out the genetic map from a cross |
| read.cross | Read data for a QTL experiment |
| replace.map | Replace the genetic map of a cross |
| ripple | Compare marker orders |
| scanone | Genome scan with a single QTL model |
| 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 |
| subset.cross | Subsetting data for QTL experiment |
| summary.cross | Print summary of QTL experiment |
| summary.fitqtl | Summary of fit of qtl model |
| summary.map | Print summary of a genetic map |
| summary.ripple | Print summary of ripple results |
| summary.scanone | Summarize the results of a genome scan |
| summary.scantwo | Summarize the results of a two-dimensional genome scan |
| switch.order | Switch the order of markers on a chromosome |
| top.errorlod | List genotypes with large error LOD scores |
| totmar | Print summary of QTL experiment |
| write.cross | Write data for a QTL experiment to a file |