profileGen {ASMap} | R Documentation |

## Profile individual genotype statistics for an R/qtl cross object

### Description

Profile individual genotype statistics for the current linkage map order of and R/qtl cross object

### Usage

```
profileGen(cross, chr, bychr = TRUE, stat.type = c("xo", "dxo",
"miss"), id = "Genotype", xo.lambda = NULL, ...)
```

### Arguments

`cross` |
An qtl |

`chr` |
Character vector of linkage group names used for subsetting the linkage map. |

`bychr` |
Logical vector determining whether statistics should be plotted by chromosome (see Details). |

`stat.type` |
Character string of any combination of |

`id` |
Character string determining the column of |

`xo.lambda` |
A numerical value for the expected rate of recombination. (see Details). |

`...` |
Other arguments to be passed to the high level lattice plot. |

### Details

This function uses `statGen`

to profile statistics for the
genotypes for the current order of the linkage map. Any combination of
`"xo"`

or `"dxo"`

or `"miss"`

may be given to
simultaneous plot. If `bychr = TRUE`

then the plots will be further partitioned by
linkage groups given by `chr`

.

If a numerical value is given for `xo.lambda`

then the
recombination count for each genotype is tested against the expected
recombination rate `xo.lambda`

using a simple one-tailed test of a
Poisson mean. Any lines that have a p-value less than than a family wise
error rate based on bonferroni adjustment of the usual alpha level of 0.05 are
annotated on the profiles being plotted.

### Value

A lattice panel plot with panels described by the `stat.type`

given
in the call and genotype statistics are returned invisibly. If
`xo.lambda`

is not NULL then these statistics also include a
logical vector named `"xo.lambda"`

that is returned from testing
the individuals for inflated recombination rates (see Details).

### Author(s)

Julian Taylor

### References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic
Linkage Map Construction and Diagnosis. Journal of Statistical Software,
**79**(6), 1–29.

### See Also

### Examples

```
data(mapDH, package = "ASMap")
## profile all genotype crossover and double crossover statistics
profileGen(mapDH, bychr = FALSE, stat.type = c("xo","dxo"),
xo.lambda = 25, layout = c(1,3))
```

*ASMap*version 1.0-7 Index]