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.
Usage
set_gene_rates(
cesa = NULL,
rates = NULL,
samples = character(),
missing_genes_take_nearest = FALSE
)Arguments
- cesa
CESAnalysis object
- rates
A two-column data.table with either gene name or protein_id in column 1 and rate in column 2
- samples
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.
- missing_genes_take_nearest
Set to TRUE to have each gene/protein_id missing from rates take the rate of the nearest non-missing gene/protein.
Details
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.