scan.haplo.2D: runs haplo.score.slide with all pairs of markers in a region
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 on all pairs of markers in a region and presents output as scan.gwaa.2D-class object

1 2	scan.haplo.2D(formula, data, snpsubset, idsubset, 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.
`bcast`	show progress every `bcast` percents of progress
`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 actual degrees of freedom of the test.

Object of class scan.gwaa.2D-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.2D-class, scan.haplo, scan.glm.2D, haplo.score.slide

if (require(haplo.stats)) {
## Not run: 
require(GenABEL.data)
data(srdta)
c <- scan.haplo.2D("bt~sex+age+CRSNP",data=srdta,snps=(717:733),
	ids=(srdta@phdata$age<40))
plot(c)

## End(Not run)
}