A function to verify the structure of a PharmacoSet

This function checks the structure of a PharamcoSet, ensuring that the correct annotations are in place and all the required slots are filled so that matching of cells and drugs can be properly done across different types of data and with other studies.

Usage

checkPsetStructure(object, plotDist = FALSE, result.dir = ".")

Arguments

object

A PharmacoSet to be verified

plotDist

Should the function also plot the distribution of molecular data?

result.dir

The path to the directory for saving the plots as a string

Value

Prints out messages whenever describing the errors found in the structure of the object object passed in.

Examples

data(CCLEsmall)
checkPsetStructure(CCLEsmall)
#> Warning: rna: rowData dimension is OK
#> Warning: rna: colData dimension is OK
#> Warning: 
#> Warning: 
#> Warning: BEST is OK
#> Warning: Symbol is OK
#> Warning: rnaseq: rowData dimension is OK
#> Warning: rnaseq: colData dimension is OK
#> Warning: 
#> Warning: 
#> Warning: rnaseq: BEST does not exist in rowData (features)
#>                                columns
#> Warning: rnaseq: Symbol does not exist in rowData (features)
#>                                columns
#> Warning: mutation: rowData dimension is OK
#> Warning: mutation: colData dimension is OK
#> Warning: 
#> Warning: 
#> Warning: cnv: rowData dimension is OK
#> Warning: cnv: colData dimension is OK
#> Warning: 
#> Warning: