summary.scantwo {qtl} | R Documentation |

Summarize the interesting aspects of the results of `scantwo`

.

summary.scantwo(object, thresholds = c(0, 0, 0), type = c("joint","interaction"), ...)

`object` |
An object of class `scantwo` , the output of the
function `scantwo` . |

`thresholds` |
A vector of length three, giving LOD thresholds for the joint LOD, interaction LOD and single-QTL conditional LOD. Negative threshold values are taken relative to the maximum joint, interaction, or individual QTL LOD, respectively. |

`type` |
Indicates whether to pick peaks with maximal joint or interaction LOD. |

`...` |
Ignored at this point. |

For each pair of chromosomes, the pair of loci for which the
LOD score (either joint or interaction LOD, according to the argument
`type`

) is a maximum is considered. The pair is printed only if
its joint LOD score exceeds the joint threshold and either (a) the
interaction LOD score exceeds its threshold or (b) both of the loci have
conditional LOD scores that are above the conditional LOD threshold,
where the conditional LOD score for locus *q1*, *LOD(q1 | q2)*, is the *log10* likelihood ratio
comparing the model with *q1* and *q2* acting
additively to the model with *q2* alone.

In the case the results of `scanone`

are not
available, the maximum locus pair for each chromosome is printed
whenever its joint LOD exceeds the joint LOD threshold.

The criterion used in this summary is due to Gary Churchill and Saunak Sen, and deserves careful consideration and possible revision.

An object of class `summary.scantwo`

, to be printed by
`print.summary.scantwo`

. Pairs of loci meeting the specified
criteria are printed, with their joint LOD, interaction LOD, and the
conditional LOD for each locus, along with single-point P-values
calculated by the *chi-square* approximation. P-values
are printed as *-log10(P)*.

If the input `scantwo`

object does not include the results of
`scanone`

, the interaction and conditional LOD thresholds are
ignored, and all pairs of loci for which the joint LOD exceeds its
threshold are printed, though without their conditional LOD scores.

Hao Wu, hao@jax.org; Karl W Broman, kbroman@jhsph.edu; Brian Yandell

`scantwo`

, `plot.scantwo`

,
`max.scantwo`

data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=5) out.2dim <- scantwo(fake.f2, method="hk") # All pairs of loci summary(out.2dim) # Pairs meeting specified criteria summary(out.2dim, c(7, 3, 3)) # Pairs with both conditional LODs > 2 summary(out.2dim,c(0,1000,2)) # Pairs with interaction LOD is above 3 summary(out.2dim,c(0,3,1000))

[Package *qtl* version 0.98-57 Index]