R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Method "boxplotSexGenotypeBatchAdjusted"

boxplotSexGenotypeBatchAdjusted

R Documentation

Method "boxplotSexGenotypeBatchAdjusted"

Description

Graph function for the phenotypic dataset. Creates a box plot split by sex and genotype after accounting for batch.

Usage

    boxplotSexGenotypeBatchAdjusted(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

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.

Examples

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

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/boxplotSexGenotypeBatchAdjusted.Rd_%03d_medium.png", width=480, height=480)
> ### Name: boxplotSexGenotypeBatchAdjusted
> ### Title: Method "boxplotSexGenotypeBatchAdjusted"
> ### Aliases: boxplotSexGenotypeBatchAdjusted
> 
> ### ** Examples
> 
>     file <- system.file("extdata", "test1.csv", package="PhenStat")
>     test <- PhenList(dataset=read.csv(file),
+             testGenotype="Sparc/Sparc")
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.

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

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

>     # box plot for dataset with two sexes: males and females
>     boxplotSexGenotypeBatchAdjusted(test,
+             depVariable="Bone.Mineral.Content",
+             graphingName="BMC" )
Information:
Bone.Mineral.Content variable is adjusted treating batch as a random effect.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>