R/extractNetworkGenes.R

In hemoshear/pathwayTalk:

#' @title extractNetworkGenes
#' @export
extractNetworkGenes <- function(network_df, pathway_list, gene_key){

    output <- c()
    results <- c()
    lengths1 <- c()
    lengths2 <- c()

    for (i in 1:nrow(network_df)){

        pathway1 <- network_df$pathway1[i]
        pathway2 <- network_df$pathway2[i]

        lengths1[i] <- length(pathway_list[[pathway1]])
        lengths2[i] <- length(pathway_list[[pathway2]])

        all_genes <- c(pathway_list[[pathway1]], pathway_list[[pathway2]])
        all_genes <- unique(all_genes)

        results[[i]] <- all_genes

    }

    names(results) <- network_df$edge
    genes_df <- stack(results)
    colnames(genes_df) <- c('entrezgene_id', 'edge')
    genes_df %<>% filter(entrezgene_id != 'None')
    genes_df %<>% left_join(key)

    len_df = data.frame('pathway1_length' = lengths1,
                        'pathway2_length' = lengths2
                        # ,
                        # 'intersection_length' = in_length
    )
    network_df <- bind_cols(network_df, len_df)

    output[['network_df']] <- network_df
    output[['genes_df']] <- genes_df

    return(output)
}