qtl (version 1.66)

mqmtestnormal: Shapiro normality test used for MQM

Description

Wraps a shapiro's normality test from the nortest package. This function is used in MQM to test the normality of the trait under investigation

Usage

mqmtestnormal(cross, pheno.col = 1,significance=0.05, verbose=FALSE)

Value

Boolean indicating normality of the trait in pheno.col. (FALSE when not normally distributed.)

Arguments

cross

An object of class cross. See read.cross for details.

pheno.col

Column number in the phenotype matrix which should be used as the phenotype. This can be a vector of integers.

significance

Significance level used in the normality test. Lower significance levels will accept larger deviations from normality.

verbose

If TRUE, print result as well as return it.

Author

Danny Arends

Details

For augmented data (as from mqmaugment), the cross is first reduced to distinct individuals. Furthermore the shapiro used to test normality works only for 3 <= nind(cross) <= 5000

See Also

• shapiro.test - Function wrapped by our mqmtestnormal

• The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf

• MQM - MQM description and references

• mqmscan - Main MQM single trait analysis

• mqmscanall - Parallellized traits analysis

• mqmaugment - Augmentation routine for estimating missing data

• mqmautocofactors - Set cofactors using marker density

• mqmsetcofactors - Set cofactors at fixed locations

• mqmpermutation - Estimate significance levels

• scanone - Single QTL scanning

Examples

data(multitrait)

# test normality of 7th phenotype
mqmtestnormal(multitrait, pheno.col=7)

# take log
multitrait <- transformPheno(multitrait, pheno.col=7, transf=log)

# test again
mqmtestnormal(multitrait, pheno.col=7)