R: runs haplo.score.slide with all pairs of markers in a region

scan.haplo.2D {GenABEL} | R Documentation

## runs haplo.score.slide with all pairs of markers in a region

### Description

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

### Usage

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

### Arguments

`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`

### Details

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.

### Value

Object of class `scan.gwaa.2D-class`

### Author(s)

Yurii Aulchenko

### References

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.

### See Also

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

### Examples

    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)
    }

[Package GenABEL version 1.8-0 Index]