scan.haplo {GenABEL} | R Documentation |

Runs `haplo.score.slide`

from the package
`haplo.stats`

and represents output as
`scan.gwaa-class`

data object

scan.haplo(formula, data, snpsubset, idsubset, n.slide = 2, bcast = 10, simulate=FALSE, trait.type, ...)

`formula` |
Formula to be used in analysis. It should be a character string following standard notation. On the left-had side, there should be outcome. On the right-hand side, covariates are liste, with "+" separating the covariates (additive action). The left- and right-hand sides are separated by "~". You should put CRSNP argument in the formula. For example "qt3~CRSNP" would analyse asociation between SNPs and trait "qt3", without any adjustment. To adjust for age and sex, use "qt3~age+sex+CRSNP". Currently, only additive effects ("+") are allowed. |

`data` |
object of calss `gwaa.data-class` |

`snpsubset` |
Index, character or logical vector with subset of SNPs to run analysis on.
If missing, all SNPs from `data` are used for analysis. |

`idsubset` |
Index, character or logical vector with subset of IDs to run analysis on.
If missing, all people from `data/cc` are used for analysis. |

`n.slide` |
Default = 2. Number of loci in each contiguous subset. The first subset is the ordered loci numbered 1 to n.slide, the second subset is 2 through n.slide+1 and so on. If the total number of loci in geno is n.loci, then there are n.loci - n.slide + 1 total subsets. |

`bcast` |
show progress every `bcast` SNPs |

`simulate` |
if simulated P-values should be generated |

`trait.type` |
Character string defining type of trait,
with values of "gaussian", "binomial", "poisson", "ordinal" (see help for
`haplo.score.slide` for details). If not specified,
the routine picks up "gaussian" or "binomial" (two levels of trait). |

`...` |
other arguments to be passed to `haplo.score.slide` |

List element P2df is set equal to P1df, as only allelic results are returned. This has nothing to do with degrees of freedom.

Object of class `scan.gwaa-class`

Yurii Aulchenko

For haplo.stats (scan.haplo, scan.haplo.2D), please cite:

Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet, 70: 425-434.

`scan.gwaa-class`

,
`haplo.score.slide`

data(srdta) a <- ccfast("bt",srdta,snps=(717:733),ids=(srdta@phdata$age<40)) plot(a) if (require(haplo.stats)) { b <- scan.haplo("bt~sex+CRSNP",srdta,snps=(717:733), ids=(srdta@phdata$age<40)) c <- scan.haplo("bt~sex+CRSNP",srdta,snps=(717:733), ids=(srdta@phdata$age<40),n.slide=3) add.plot(b,col="red",type="l") add.plot(c,col="darkgreen",type="l") }

[Package *GenABEL* version 1.6-7 Index]