ValidateGeneSet: Conducts cross validation to test for diffusion proximity of...
In lancour/ignition: INTEGRATION OF GENETIC ASSOCIATIONS WITH NETWORK DIFFUSION

Description Usage Arguments Value Examples

Our methodology assumes that the phenotype-related genes for the phenotype of interest actually have a significantly closer than random proximity to one another. This function is used to test this assumption for any set of genes.

1	ValidateGeneSet(kernel, pheno.gene.set, autocaps = TRUE)

`kernel`	Required. A square, symmetrical distance kernel. `CreateKernel` will produce this but the user may provide their own kernel. If you are using your own kernel, make sure to have set the row and column names of the matrix to gene symbols.
`pheno.gene.set`	Required. A character vector of genes that represent the previously known phenotype-related genes. The function will test for proximity between these genes. This set will automatically be coerced to uppercase unless overriden (see autocaps param)
`autocaps`	Optional. Defaults to TRUE. Converts the provided gene set to uppercase to coincide with the upper case format used for gene identifiers.

A data frame containing the cross validation percentiles for each gene.

data(ignition.example.edges)
adj.matrix = CreateAdjMatrix(ignition.example.edges)
kernel = CreateKernel(adj.matrix)
nonproximal.gene.set = c('B', 'I', 'F')
proximal.gene.set = c('D', 'B', 'A')
ValidateGeneSet(kernel, nonproximal.gene.set)
ValidateGeneSet(kernel, proximal.gene.set)