scan.haplo: scan.haplo
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

Runs haplo.score.slide from the package haplo.stats and represents output as scan.gwaa-class data object

1 2	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

require(GenABEL.data)
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")
}