scan.glm {GenABEL} | R Documentation |
Scan GWA data using glm
scan.glm(formula, family = gaussian(), data, snpsubset, idsubset, bcast = 50)
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 |
Object of class scan.gwaa-class
Yurii Aulchenko
ccfast
,
qtscore
,
scan.gwaa-class
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