mqmtestnormal: Shapiro normality test used for MQM

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/mqmutil.R

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

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

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.

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

Value

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

Author(s)

Danny Arends danny.arends@gmail.com

See Also

Examples

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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)

qtl documentation built on June 20, 2017, 9:05 a.m.