PhenList-class: Class "PhenList"

Description

A list-based S4 class for storing phenotypic data. Helps to support data integrity checks and statistics calculation. The PhenList object can be created by using function PhenList.

Arguments

Explore PhenList object

PhenList object instance contains the following slots: 1. "datasetPL" where cleaned and checked dataset is stored: getDataset(phenList) 2. "testGenotype" where the genotype level to test is stored: testGenotype(phenList) 3. "refGenotype" where reference genotype value is stored with default value set to "+/+": refGenotype(phenList) 4. "hemiGenotype" if defined contains the genotype value for hemizygous: hemiGenotype(phenList) 6. "dataset.clean" flag value is stored, see PhenList for more details: phenList@dataset.clean 7. "dataset.colname" if defined contains dataset column names that have been renamed: - phenList@dataset.colname.batch column name for batch values - phenList@dataset.colname.genotype column name for genotype values - phenList@dataset.colname.sex column name for sex values - phenList@dataset.colname.weight column name for weight values 8. "dataset.values" if defined contains dataset values that have been changed during dataset cleaning process: - phenList@dataset.values.missingValue value used as missing value in the orginal dataset - phenList@dataset.values.male value used to label "males" in the original dataset - phenList@dataset.values.female value used to label "females" in the original dataset

Slots

datasetPL:: Object of class "data.frame" ~~ dataset to work with
refGenotype:: Object of class "character" ~~ reference genotype
testGenotype:: Object of class "character" ~~ test genotype
hemiGenotype:: Object of class "character" ~~ hemi genotype
dataset.colname.batch:: Object of class "character" ~~ column name for batch values
dataset.colname.genotype:: Object of class "character" ~~ column name for genotype values
dataset.colname.sex:: Object of class "character" ~~ column name for sex values
dataset.colname.weight:: Object of class "character" ~~ column name for weigth values
dataset.values.missingValue:: Object of class "character" ~~ value used as missing value in the orginal dataset
dataset.values.male:: Object of class "character" ~~ value used to label "males" in the original dataset
dataset.values.female:: Object of class "character" ~~ value used to label "females" in the original dataset
dataset.clean:: Object of class "logical" ~~ flag value is stored
datasetUNF:: Object of class "data.frame" ~~ unfiltered dataset

Methods

getDataset: (accessor): Returns dataset
refGenotype: (accessor): Returns reference genotype
testGenotype: (accessor): Returns test genotype
hemiGenotype: (accessor): Returns hemi genotype if specified
getColumn: Returns specified column if exists
getColumnBatchAdjusted: Returns specified column adjusted for batch effect
getColumnWeightBatchAdjusted: Returns specified column adjusted for batch and weight effects
getStat: Returns simple dataset statistics
getVariables: Returns dataset column names
batchIn: Returns TRUE if the batch is in the dataset, FALSE otherwise
weightIn: Returns TRUE if the weight is in the dataset, FALSE otherwise
multipleBatches: Returns TRUE if the batches are variable in the dataset, FALSE otherwise
noSexes: Returns number of sexes in the dataset
setBatch: Sets the batch column - change the column names
setGenotype: Sets the genotype column - change the column names
setMissingValue: Sets the missing value
setSex: Sets the sex column - change the column names
setWeight: Sets the weight column - change the column names

Examples

Run this code

    file <- system.file("extdata", "test1.csv", package="PhenStat")
    test <- PhenList(dataset=read.csv(file),
            testGenotype="Sparc/Sparc")
    class(test)
    
    file <- system.file("extdata", "test2.csv", package="PhenStat")
    test2 <- PhenList(dataset=read.csv(file),
            testGenotype="Arid4a/Arid4a",
            refGenotype="+/+",
            hemiGenotype="Arid4a/+",
            dataset.colname.weight="Weight.Value")
    getStat(test2)
    testGenotype(test2)
    refGenotype(test2)
    hemiGenotype(test2)