R: Shapiro normality test used for MQM

mqmtestnormal {qtl} | R Documentation

## 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)

### 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

- `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)

[Package qtl version 1.46-2 Index]