Shapiro normality test used for MQM
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
mqmtestnormal(cross, pheno.col = 1,significance=0.05, verbose=FALSE)
cross |
An object of class |
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. |
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 danny.arends@gmail.com
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
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)
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