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
An object of class
Column number in the phenotype matrix which should be used as the phenotype. This can be a vector of integers.
Significance level used in the normality test. Lower significance levels will accept larger deviations from normality.
If TRUE, print result as well as return it.
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
Boolean indicating normality of the trait in pheno.col. (FALSE when not normally distributed.)
Danny Arends [email protected]
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
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