View source: R/gene_mutation_rates.R
gene_mutation_rates | R Documentation |
This function calculates gene-level neutral mutation rates based on counts of nonsynonymous and synonymous mutations per gene under the dNdScv package's model, as described in Martincorena et al.
gene_mutation_rates(
cesa,
covariates = NULL,
samples = character(),
dndscv_args = list(),
save_all_dndscv_output = FALSE
)
cesa |
CESAnalysis object |
covariates |
Tissue-specific mutation rate covariates. Typically, supply the covariates object from your refset (e.g., ces.refset.hg19$covariates$bladder), or the object name ("bladder"). Run list_ces_covariates() to see choices. For hg19 data only, set to "hg19" to use dNdScv's non-tissue-specific covariates. If no appropriate covariates data are available, set to NULL to run without. Finally, you can also supply custom covariates data in the form of a matrix or prcomp object (see website for details). |
samples |
Which samples to include in the current run. Defaults to all samples. Can be a vector of Unique_Patient_Identifiers, or a data.table containing rows from the CESAnalysis sample table. |
dndscv_args |
Custom arguments to pass to dNdScv. (The arguments |
save_all_dndscv_output |
Default FALSE; when TRUE, saves all dndscv output, not just what's needed by cancereffectsizeR. (Full output can be very large, in the gigabytes.) |
CESAnalysis object with gene-level mutation rates calculated
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