R: Scan GWA data using glm

scan.glm {GenABEL} | R Documentation

## Scan GWA data using glm

### Description

Scan GWA data using glm

### Usage

    scan.glm(formula, family = gaussian(), data, snpsubset, idsubset,
    		bcast = 50)

### Arguments

`formula` | character string containing formula to be used in `glm`. You should put CRSNP argument in the formula, to arrange how the SNP from the list would be treated. This allows to put in an interaction term.
`family` | family to be passed to `glm`
`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.
`data` | object of class "gwaa.data"
`bcast` | show progress every `bcast` SNPs

### Value

Object of class `scan.gwaa-class`

### Author(s)

Yurii Aulchenko

### See Also

`ccfast`, `qtscore`, `scan.gwaa-class`

### Examples

    require(GenABEL.data)
    data(srdta)
    a <- scan.glm("bt~sex+age+CRSNP",family=binomial(),data=srdta,snps=(1:10),bcast=2)
    #plot(a)

    osnp <- "rs4934"
    maposnp <- srdta@gtdata@map[osnp]
    maposnp
    reg <- snp.names(srdta,begin=maposnp-100000,end=maposnp+100000,chrom="1")
    ## Not run:
    a <- scan.glm("qt3~sex+age+CRSNP",data=srdta,snps=reg)
    plot(a)
    plot(a,df=1)
    add.plot(a,df=2)

    ## End(Not run)

    # interaction with sex
    ## Not run:
    a <- scan.glm("qt3~age+sex*CRSNP",data=srdta,snps=reg)
    plot(a,df=1)
    add.plot(a,df=2)
    # you can do interaction with a selected polymorphisms in the same way

    ## End(Not run)

[Package GenABEL version 1.8-0 Index]