add.expression.R

#' Add Gene Expression
#' @description This function adds the gene expression values to each "case_id" of a gene in the data frame. It uses the expressionmatrix from organ_data.
#' @param cancer_data A large list created by multimodalR
#' @param nested_metadata A list of data frames made by >make.nested.metadata<
#' @param key Character or integer - Column name or index of unique identifier of nested_metadata, default = "case_id"
#' @importFrom magrittr %>%
#' @examples
#' lungMetaExpression <- add.expression(lungXY, lungMetaExpression)
#' @return Returns the same list but with data franes containing the expression values in a new colummn.


add.expression <- function(cancer_data, nested_metadata, key = "case_id") {                                #nested_metadata = List of metadata for each gene
  for (gene in names(nested_metadata)) {
    geneExpression <- cancer_data$Expressionmatrix[gene, c(nested_metadata[[gene]][[key]])] %>% as.numeric #[genename, case_id from the matrix]
    nested_metadata[[gene]]$expression <- geneExpression                                                   #add the expression values to the data.table
  }
  return(nested_metadata)
}