boxplotSexGenotypeBatch {PhenStat} | R Documentation

## Method "boxplotSexGenotypeBatch"

### Description

NB! Function is deprecated, please use scatterplotSexGenotypeBatch function instead. Graph function for the phenotypic dataset. Creates a box plot split by sex, genotype and batch.

Note: the batches are not ordered with time but allow assessment of how the treatment groups lie relative to the normal control variation.

### Usage

        boxplotSexGenotypeBatch(phenList,
    							depVariable=NULL,
    							graphingName=NULL,
    							outputMessages=TRUE)

### Arguments

`phenList` | instance of the `PhenList` class; mandatory argument
`depVariable` | a character string defining the dependent variable of interest; mandatory argument
`graphingName` | a character string defining the name to be used on the graph for the dependent variable; mandatory argument
`outputMessages` | flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE

### Value

Empty.

### Author(s)

Natalja Kurbatova, Natasha Karp, Jeremy Mason

### References

Karp N, Melvin D, Sanger Mouse Genetics Project, Mott R (2012): Robust and Sensitive Analysis of Mouse Knockout Phenotypes. PLoS ONE 7(12): e52410. doi:10.1371/journal.pone.0052410

West B, Welch K, Galecki A (2007): Linear Mixed Models: A practical guide using statistical software New York: Chapman & Hall/CRC 353 p.

### See Also

`PhenList`

### Examples

        file <- system.file("extdata", "test1.csv", package="PhenStat")
        test <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
                testGenotype="Sparc/Sparc")
        # box plot for dataset with two sexes: males and females
        PhenStat:::boxplotSexGenotypeBatch(test,
                depVariable="Bone.Mineral.Content",
                graphingName="BMC" )

        file <- system.file("extdata", "test4.csv", package="PhenStat")
        test_1sex <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
                testGenotype="Mysm1/+")
        # box plot for females only dataset
        PhenStat:::boxplotSexGenotypeBatch(test_1sex,depVariable="Lean.Mass",
                graphingName="Lean Mass")

[Package PhenStat version 2.18.0 Index]