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Information adjacency matrix

inf_adj_matrix.Rd

Creates an adjacency matrix of shared information content/contribution between studies.

Usage

inf_adj_matrix(data, contribution = FALSE, unique = TRUE, as_list = FALSE)

Arguments

data

Data frame in the format of ARDSMAICR::data_genes

contribution

Return the information contribution -- Default = FALSE

unique

Include information for genes uniquely identified by a study -- Default = TRUE

as_list

Option to return an adjacency list -- Default = FALSE

Value

A matrix with the dimensions n studies x n studies. Where the cells represent the summed scores of genes shared between studies. Direction is maintained, columns to rows represents the information in the column shared with the row. The return may be specified as the information content - all gene scores regardless of their contribution to the MAIC score - or the information contribution - only gene scores where the study contributes to the MAIC score for that gene. The option to include or remove information content/contribution generated by a study uniquely is available.

Details

Input columns for data_genes should be (this is the standard output of the MAIC algorithm):

  • gene - HGNC gene symbol - chr

  • 1...

  • uID - Study unique identifier. Column contains study specific gene score - dbl

  • n...

  • maic_score - MAIC score for gene - dbl

  • contributors - Studies contributing to MAIC score by method - chr

Examples

if (FALSE) {
if(interactive()){
 inf_agj_matrix(ARDSMAICR::data_genes, contribution = TRUE, unique = FALSE)
 }
}