revolver_fit | R Documentation |
This function implements the main fitting function for REVOLVER, which is a 2-steps algorithm described in the REVOLVER paper (Caravagna et al., Nature Methods volume 15, pages 707–714, 2018; https://www.nature.com/articles/s41592-018-0108-x).
To run the fit the cohort needs not to throw any error when function revolver_check_cohort
is run with parameter stopOnError = TRUE
. The trees of the patients need to be computed as well.
The output object contains a new field '$fit' which contains the fit results, and is of a new S3 class called 'rev_cohort_fit' which has its own S3 methods.
revolver_fit(x, initial.solution = 1, max.iterations = 10, n = 10, ...)
x |
A REVOLVER cohort where trees per patient have been already computed. |
initial.solution |
Either a scalar to fix one initial condition
(rank id), or |
max.iterations |
Maximum number of EM steps before forcing stop. |
n |
Number of initial conditions sampled to compute optimal fit. |
... |
Parameters forwarded to a |
A new object of class "rev_cohort_fit"
which represents a
REVOLVER cohort object with fits available.
Caravagna et al., Nature Methods volume 15, pages 707–714, 2018; https://www.nature.com/articles/s41592-018-0108-x
Other Analysis functions:
revolver_cluster()
# Data released in the 'evoverse.datasets' data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets') revolver_fit(TRACERx_NEJM_2017_REVOLVER)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.