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

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")
a <- scan.glm("qt3~sex+age+CRSNP",data=srdta,snps=reg)
#plot(a)
#plot(a,df=1)
#add.plot(a,df=2)

# interaction with sex
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

[Package GenABEL version 1.6-7 Index]