scan.haplo {GenABEL} | R Documentation |
Runs haplo.score.slide
from the package
haplo.stats
and represents output as
scan.gwaa-class
data object
scan.haplo(formula, data, snpsubset, idsubset, n.slide = 2, bcast = 10, simulate=FALSE, trait.type, ...)
formula |
Formula to be used in analysis. It should be a character string following standard notation. On the left-had side, there should be outcome. On the right-hand side, covariates are liste, with "+" separating the covariates (additive action). The left- and right-hand sides are separated by "~". You should put CRSNP argument in the formula. For example "qt3~CRSNP" would analyse asociation between SNPs and trait "qt3", without any adjustment. To adjust for age and sex, use "qt3~age+sex+CRSNP". Currently, only additive effects ("+") are allowed. |
data |
object of calss gwaa.data-class |
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. |
n.slide |
Default = 2. Number of loci in each contiguous subset. The first subset is the ordered loci numbered 1 to n.slide, the second subset is 2 through n.slide+1 and so on. If the total number of loci in geno is n.loci, then there are n.loci - n.slide + 1 total subsets. |
bcast |
show progress every bcast SNPs |
simulate |
if simulated P-values should be generated |
trait.type |
Character string defining type of trait,
with values of "gaussian", "binomial", "poisson", "ordinal" (see help for
haplo.score.slide for details). If not specified,
the routine picks up "gaussian" or "binomial" (two levels of trait). |
... |
other arguments to be passed to haplo.score.slide |
List element P2df is set equal to P1df, as only allelic results are returned. This has nothing to do with degrees of freedom.
Object of class scan.gwaa-class
Yurii Aulchenko
For haplo.stats (scan.haplo, scan.haplo.2D), please cite:
Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet, 70: 425-434.
scan.gwaa-class
,
haplo.score.slide
data(srdta) a <- ccfast("bt",srdta,snps=(717:733),ids=(srdta@phdata$age<40)) b <- scan.haplo("bt~sex+CRSNP",srdta,snps=(717:733), ids=(srdta@phdata$age<40)) c <- scan.haplo("bt~sex+CRSNP",srdta,snps=(717:733), ids=(srdta@phdata$age<40),n.slide=3) plot(a) add.plot(b,col="red",type="l") add.plot(c,col="darkgreen",type="l")