Scan GWA data using glm

Description

Scan GWA data using glm

Usage

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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

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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)

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