cim.peak {eqtl} | R Documentation |
Use the LOD peaks previously detected in a peak
object to define the additive covariates and perform a single genome scan taking cofactors into account.
cim.peak(cross,peak)
cross |
An object of class cross . See 'qtl' package manual for read.cross function details. |
peak |
An object of class peak . See define.peak function for details. |
Perform a composite interval mapping using the scanone
function with additive covariates previously defined in the related peak object.
A scan is performed for traits which are affected by at least one QTL. The additive covariates for each trait are defined as the closest flanking marker to each significant LOD peak (defined in the peak feature peak_cM
). Each trait scan generates a scanone
object which is concatenated to the others scanone
objects.
Return an object of class scanone
.
Hamid A. Khalili
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890
define.peak
,c.scanone
,scanone
,find.flanking
data(seed10); seed10 <- calc.genoprob( cross=seed10, step=2, off.end=0, error.prob=0, map.function='kosambi', stepwidth='fixed'); seed10 <- sim.geno( cross=seed10, step=2, off.end=0, error.prob=0, map.function='kosambi', stepwidth='fixed'); out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='em'); out.peak <- define.peak(out.em, 'all'); out.cem <- cim.peak(seed10,out.peak);