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This function allows you to specify regional rates of mutation--calculated however you like--to samples in your CESAnalysis. Rates can be assigned to all samples or to specified samples.


  cesa = NULL,
  rates = NULL,
  samples = character(),
  missing_genes_take_nearest = FALSE



CESAnalysis object


A two-column data.table with either gene name or protein_id in column 1 and rate in column 2


Which samples the input rates apply to. Defaults to all samples. Can be a vector of Unique_Patient_Identifiers, or a data.table containing rows from the CESAnalysis sample table.


Set to TRUE to have each gene/protein_id missing from rates take the rate of the nearest non-missing gene/protein.


Provide rates in a data.table with two columns: gene name or protein ID (character) and rate (numeric, non-negative). Gene names or protein IDs must match those in CESAnalysis reference data. (Some reference data sets, such as ces.refset.hg19, only allow gene-level rates.) If you don't want to supply rates for every gene, set missing_genes_take_nearest = T to have each missing gene or coding region take the rate of the nearest non-missing one.