checkDataset: Method "checkDataset"

In PhenStat: Statistical analysis of phenotypic data

Description

Checks dataset for the minimum required info:

1. Column names should present

2. Genotype column should present

3. Sex column should present

4. Two data points for each Genotype/Sex combination

5. Number of Genotype levels should be 2

6. Number of Sex levels should be 1 or 2

7. Sex levels have to be "Female" and/or "Male"

8. Records with reference genotype should be in the dataset

9. Records with test genotype should be in the dataset

Perform the following additional checks:

- presence of Weight column,

- presence of Batch column (Assay.Date).

Warning given in case of missed data indicating that you can only fit a glm or to use MM equation "withoutWeight".

Function checkDataset is called from PhenList function.

Usage

    checkDataset(dataset, 
				testGenotype, 
				refGenotype="+/+",
				outputMessages=TRUE,
				dataset.clean=TRUE) 
    

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 "+/+"
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

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

PhenTestResult

Examples

    
    # "checkDataset" is called internally from "PhenList" function
    file <- system.file("extdata", "test1.csv", package="PhenStat")
    test <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
            testGenotype="Sparc/Sparc")    
    

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