qb.confound {qtlbim} | R Documentation |
Covariates used in gene mapping may be correlated with covariates. These routines examine the pattern of confounding.
qb.confound(qbObject, covar = 1) ## S3 method for class 'qb.confound': plot(x, ylim, main, ...) ## S3 method for class 'qb.confound': print(x, ...) ## S3 method for class 'qb.confound': summary(object, ...)
qbObject |
Object of class qb . |
x |
Object of class qb.confound . |
object |
Object of class qb.confound . |
covar |
Index to covariate |
ylim |
Limits for y (vertical) plotting axis. |
main |
Title for plot. |
... |
Additional parameters passed alone. |
This examines possible confounding between a covariate and pseudomarkers across the genome. Confouding, evidenced by large correlation with a marker, would raise suspicions about mapping in a genomic region, unless of course the covariate is a marker in that region. Blue curves are correlation with additive effect; red curves are correlation with dominance effect. Dashed lines at 5 percent significance limits.
qb.confound
returns a matrix with columns for:
coradd |
Correlation with additive pseudomarker effect. |
cordom |
Correlation with dominance pseudomarker effect (if F2). |
chr |
Chromosome identifier. |
The object inherits from scanone
objects.
Brian S. Yandell
http://www.qtlbim.org
data(qbExample) temp <- qb.confound(qbExample) plot(temp)