qb.confound {qtlbim} | R Documentation

## Examine confounding of covariate with pseudomarkers.

### Description

Covariates used in gene mapping may be correlated with covariates. These routines examine the pattern of confounding.

### Usage

    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, ...)

### Arguments

`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.

### Details

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.

### Value

`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.

### Author(s)

Brian S. Yandell

### References

http://www.qtlbim.org

### See Also

`qb.mcmc`

### Examples

    temp <- qb.confound(qbExample)
    plot(temp)

[Package qtlbim version 1.6.5 Index]