Description Usage Arguments Value
execute bayesNMF for signature deconvolution
1 2 3 | run_bayesNMF(mat, tumor.type = "tumor.type", max_k = 10, n_runs = 10,
iter_per_run = 1e+05, tol = 1e-07, a0 = 10, phi = 1, prior = "L1KL",
hyper = FALSE)
|
mat |
(matrix) N*M matrix of ints with N mutation frequencies for each of M samples |
max_k |
(int) max hypothesized number of signatures to look for. default: 10 |
n_runs |
(int) number of times to run optimization code. default: 10 |
iter_per_run |
(int) number of iter for each run. default: 100000 |
tol |
(float) tolerance used to assess convergence |
a0 |
(int) value of hyperparameter 'a'. default: 10 |
phi |
(int) value of hyperparameter 'phi'. default: 1 (appropriate for l1-loss with exponential prior) |
prior |
(chr) either L1KL (expoential priors) or L2KL (half-normal priors). default: L1KL |
hyper |
(logical) if TRUE, reduce the effect of hyper-mutant samples in the signature discovery. default: FALSE |
tumor_name |
(chr) name of tumor, used for plotting headers, etc. default: 'tumor.type' |
list of signatures, where each signature is a named list containing plots & data
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.