This function provides an interface to software SigProfiler. More please see https://github.com/AlexandrovLab/SigProfilerExtractor. Typically, a reference genome is not required because the input is a matrix (my understanding).
sigprofiler_extract( nmf_matrix, output, range = 2:5, nrun = 10L, refit = FALSE, refit_plot = FALSE, is_exome = FALSE, init_method = c("nndsvd_min", "random", "alexandrov-lab-custom", "nndsvd", "nndsvda", "nndsvdar"), cores = -1L, genome_build = c("hg19", "hg38", "mm10", "mm9"), use_conda = FALSE, py_path = NULL, sigprofiler_version = "1.1.3" ) sigprofiler_import( output, order_by_expo = FALSE, type = c("suggest", "refit", "all") )
nmf_matrix | a |
---|---|
output | output directory. |
range | signature number range, i.e. |
nrun | the number of iteration to be performed to extract each signature number. |
refit | if |
refit_plot | if |
is_exome | if |
init_method | the initialization algorithm for W and H matrix of NMF. Options are 'random', 'nndsvd', 'nndsvda', 'nndsvdar', 'alexandrov-lab-custom' and 'nndsvd_min'. |
cores | number of cores used for computation. |
genome_build | I think this option is useless when input is |
use_conda | if |
py_path | path to Python executable file, e.g. '/Users/wsx/anaconda3/bin/python'. |
sigprofiler_version | version of |
order_by_expo | if |
type | one of 'suggest' (for suggested solution), 'refit' (for refit solution) or 'all' (for all solutions). |
For sigprofiler_extract()
, returns nothing. See output
directory.
For sigprofiler_import()
, a list
containing Signature
object.
if (FALSE) { load(system.file("extdata", "toy_copynumber_tally_W.RData", package = "sigminer", mustWork = TRUE )) reticulate::conda_list() sigprofiler_extract(cn_tally_W$nmf_matrix, "~/test/test_sigminer", use_conda = TRUE ) sigprofiler_extract(cn_tally_W$nmf_matrix, "~/test/test_sigminer", use_conda = FALSE, py_path = "/Users/wsx/anaconda3/bin/python" ) }