checkDataset {PhenStat} | R Documentation

## Method "checkDataset"

### 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")

[Package PhenStat version 2.28.0 Index]