Last data update: 2014.03.03

R: Method "qqplotRotatedResiduals"
qqplotRotatedResidualsR Documentation

Method "qqplotRotatedResiduals"

Description

Graph function for the Mixed Model framework's results. Creates a Q-Q plot of rotated residuals.

Usage

    qqplotRotatedResiduals(phenTestResult,outputMessages=TRUE)

Arguments

phenTestResult

instance of the PhenTestResult class that comes from the function testDataset; mandatory argument

outputMessages

flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE

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

Houseman, E. A., Ryan, L. M., Coull, B. A. (2004): Cholesky residuals for assessing normal errors in a linear model with correlated outcomes. Journal of the American Statistical Association 99466: pg 383-394. Doi 10.1198

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 and PhenTestResult

Examples

    file <- system.file("extdata", "test2.csv", package="PhenStat")
    test <- PhenList(dataset=read.csv(file),
            dataset.colname.weight="Weight.Value",
            testGenotype="Arid4a/Arid4a",
            hemiGenotype="Arid4a/+")
    result <- testDataset(test,
            depVariable="Cl")
    qqplotRotatedResiduals(result)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PhenStat)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PhenStat/qqplotRotatedResiduals.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qqplotRotatedResiduals
> ### Title: Method "qqplotRotatedResiduals"
> ### Aliases: qqplotRotatedResiduals
> 
> ### ** Examples
> 
>     file <- system.file("extdata", "test2.csv", package="PhenStat")
>     test <- PhenList(dataset=read.csv(file),
+             dataset.colname.weight="Weight.Value",
+             testGenotype="Arid4a/Arid4a",
+             hemiGenotype="Arid4a/+")
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.

Warning:
Hemizygotes 'Arid4a/+' have been relabelled to test genotype 'Arid4a/Arid4a'.
If you don't want this behaviour then don't define 'hemiGenotype' argument.

Information:
Dataset's 'Genotype' column has following values: '+/+', 'Arid4a/Arid4a'

Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'

>     result <- testDataset(test,
+             depVariable="Cl")
Information:
Dependent variable: 'Cl'.

Information:
Perform all MM framework stages: startModel and finalModel.

Information:
Method: Mixed Model framework.

Information:
Equation: 'withWeight'.

Information:
Calculated values for model effects are: keepBatch=TRUE, keepEqualVariance=TRUE, keepWeight=TRUE, keepSex=FALSE, keepInteraction=FALSE.

>     qqplotRotatedResiduals(result)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>