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| A starting point | Introductory comments |
| argmax.geno | Reconstruct underlying genotypes |
| calc.errorlod | Identify likely genotyping errors |
| calc.genoprob | Calculate conditional genotype probabilities |
| clean | Remove intermediate calculations |
| 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 |
| drop.qtlgeno | Remove QTL genotypes |
| est.map | Estimate genetic maps |
| est.rf | Estimate pairwise recombination fractions |
| fake.4way | Simulated data for a 4-way cross experiment |
| fake.bc | Simulated data for a backcross experiment |
| fake.f2 | Simulated data for an F2 intercross experiment |
| find.errors | Identify likely genotyping errors |
| geno.table | Create table of genotype distributions |
| hyper | Data on hypertension |
| listeria | Data on Listeria monocytogenes susceptibility |
| nchr | Print summary of QTL experiment |
| nind | Print summary of QTL experiment |
| nmar | Print summary of QTL experiment |
| nphe | Print summary of QTL experiment |
| plot.cross | Plot various features of a cross object |
| plot.errorlod | Plot grid of error LOD values |
| plot.errors | Plot grid of likely genotyping errors |
| plot.geno | Plot genotypes with indication of likely errors |
| plot.info | Plot the proportion of missing information in the genotype data |
| plot.map | Plot genetic map |
| plot.missing | Plot grid of missing genotypes |
| plot.rf | Plot recombination fractions |
| plot.scanone | Plot output for a single QTL scan |
| pull.chr | Pull out a subset of chromosomes from a cross |
| pull.map | Pull out the genetic map from a cross |
| read.cross | Read data for a QTL experiment |
| read.cross.csv | Read data for a QTL experiment in comma-delimited format |
| read.cross.gary | Read data for a QTL experiment in Gary Churchill's format |
| read.cross.karl | Read data for a QTL experiment in Karl Broman's format |
| read.cross.mm | Read data for a QTL experiment in mapmaker format |
| replace.map | Replace the genetic map of a cross |
| ripple | Compare marker orders |
| scanone | Genome scan with single QTL model |
| scanone.perm | Permutation test for genome scan with single QTL model |
| sim.cross | Simulate a QTL experiment |
| sim.geno | Simulate genotypes given observed marker data |
| sim.map | Simulate a genetic map |
| summary.cross | Print summary of QTL experiment |
| summary.ripple | Print summary of ripple results |
| summary.scanone | Print summary of the scanone output |
| switch.order | Switch the order of markers on a chromosome |
| top.errorlod | List genotypes with highest error LOD values |
| totmar | Print summary of QTL experiment |
| vbscan | Genome scan for trait with some undefined values |
| vbscan.perm | Permutation test for trait with some undefined values |
| write.cross | Write data for a QTL experiment to a file |
| write.cross.csv | Write data in comma-delimited format |
| write.cross.mm | Write data in mapmaker format |