PhenList: Method "PhenList"

In PhenStat: Statistical analysis of phenotypic data

Description

Function to create data object from the data frame.

In addition to dependent variable column (the variable of interest) mandatory columns that should present in the data frame are "Genotype" and "Sex". The "Assay.Date" column is used to model "Batch" effect if not specified differently. "Weight" column is used to model body weight effect.

Function creates PhenList object, checks data integrity, renames columns when requested, provides simple statistics about dataset.

Returns an instance of the PhenList object created from the data file.

Dataset is cleaned to ensure there is a maximum two sex levels and there are exactly two levels for genotype. Data cleaning can be switched off by defining the argument "dataset.clean" as FALSE.

Usage

    PhenList(dataset, testGenotype, refGenotype="+/+", hemiGenotype=NULL,
            outputMessages=TRUE, dataset.clean=TRUE,
            dataset.colname.batch=NULL, dataset.colname.genotype=NULL,
            dataset.colname.sex=NULL, dataset.colname.weight=NULL,
            dataset.values.missingValue=" ", dataset.values.male=NULL,
            dataset.values.female=NULL)

Arguments

dataset	data frame created from file or from another source; mandatory argument
testGenotype	defines the test genotype to be compared to the reference genotype; mandatory argument
refGenotype	defines the reference genotype; assigned default value is "+/+"
hemiGenotype	defines the genotype value for hemizygous that will be changed to test genotype value
outputMessages	flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; assigned default value is TRUE
dataset.clean	flag: "FALSE" value for no modification of the dataset; "TRUE" value to clean dataset if needed; assigned default value is TRUE
dataset.colname.batch	column name within dataset for the batch effect
dataset.colname.genotype	column name within dataset for the genotype info
dataset.colname.sex	column name within dataset for the sex info
dataset.colname.weight	column name within dataset for the weight info
dataset.values.missingValue	value used as missing value in the dataset
dataset.values.male	value used to label "males" in the dataset
dataset.values.female	value used to label "females" in the dataset

Value

Returns an instance of the PhenList class.

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")

    file <- system.file("extdata", "test2.csv", package="PhenStat")
    test2 <- PhenStat:::PhenList(dataset=read.csv(file, na.strings = '-'),
            testGenotype="Arid4a/Arid4a",
            refGenotype="+/+",
            hemiGenotype="Arid4a/+",
            dataset.colname.weight="Weight.Value")

    file <- system.file("extdata", "test3.csv", package="PhenStat")
    test3 <- PhenStat:::PhenList(dataset=read.csv(file, na.strings = '-'),
            dataset.clean=TRUE,
            dataset.values.female=1,
            dataset.values.male=2,
            testGenotype="Mysm1/+")

PhenStat documentation built on Nov. 8, 2020, 8:13 p.m.