scan.glm: Scan GWA data using glm

In GenABEL: genome-wide SNP association analysis

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)

GenABEL documentation built on May 30, 2017, 3:36 a.m.