A function to verify the structure of a CoreSet

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 samples and drugs can be properly done across different types of data and with other studies.

Usage

checkCsetStructure(object, plotDist = FALSE, result.dir = tempdir())

Arguments

object

A CoreSet 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. Defaults to this R sessions tempdir().

Value

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

Examples

checkCsetStructure(clevelandSmall_cSet)
#> [1] "rna sampleid does not exist in colData (samples)\nrnaseq sampleid does not exist in colData (samples)\nunique.sampleid which is curated sample id across data set should be a column of sample curation slot"