Function reference • ARDSMAICR

Datasets

data_study: Study metadata - ARDS MAIC Update 1.0.0

data_genes: Overall ARDS MAIC results - ARDS MAIC Update 1.0.0

data_contributions: Overall gene list contributions - ARDS MAIC Update 1.0.0

data_biolitmine: BioLitMine results - ARDS MAIC Update 1.0.0

data_covidmaic: SARS-CoV-2 MAIC genes - ARDS MAIC Update 1.0.0

Summary tables

design_table(): Create a table of study designs

methods_table(): Create a table of study methods

gene_table(): Table of genes

Helper functions - counts

count_genes(): Count total number of genes

count_lists(): Count total number of gene lists

Helper functions - genes

genes_per_list(): Count number of genes by gene list

genes_per_method(): Count number of genes by method

genes_per_category(): Count number of genes by category

Helper functions - lists

lists_per_gene(): Count number of gene lists supporting each gene

lists_per_method(): Count number of gene lists by method

lists_per_method_per_gene(): Count number of gene lists by method by gene

lists_per_category(): Count number of gene lists by category

lists_per_category_per_gene(): Count number of gene lists by category by gene

Helper functions - methods and categories

methods_per_gene(): Count number of methods supporting each gene

categories_per_gene(): Count number of categories supporting each gene

methods_upset(): Methods upset plot

categories_upset(): Categories upset plot

Gene prioritisation

inflection_point(): Calculate the inflection point

inflection_point_plot(): Plot the inflection point

Information content and contribution

contributions_calculation(): Calculate study contributions

inf_adj_matrix(): Information adjacency matrix

normalise_gene_scores(): Normalise gene scores