Description Usage Arguments Details Value
The parameters are identical to those for the command line bash arguments. Please see the SDA manual for the descriptions. NB Not all parameters are implemented here.
1 2 3 4 5 | run_SDA(sda_location = "sda", out = NULL, data = NULL, N = NULL,
num_comps = 10, max_iter = 500, save_freq = NULL,
free_freq = NULL, set_seed = NULL, ignore_missing = FALSE,
remove_zero_comps = TRUE, eigen_parallel = FALSE, num_blocks = 1,
num_openmp_threads = 1, save_everything = FALSE, debug = FALSE)
|
sda_location |
string; location of the sda executable e.g. "../SDA/build/sda" the default value 'sda' assumes the location of sda is in your $PATH variable |
out |
string; name of folder to be created to put results in |
data |
string; name of exported file with data in, should be equal to the value you set as the 'name' parameter for export_data. |
N |
int; number of individuals, will be inferred automatically by numer of lines in data file if not provided but this will only work if the data is 2D / a single tissue type / data / omic type! |
num_comps |
int; how many components to infer (maximum). |
max_iter |
int; maximum number of iterations to run for. |
save_freq |
int; results will be saved every save_freq iterations. Defaults to max_iter/2 |
free_freq |
int; free energy will be calculated every free_freq ierations. Defaults to max_iter/20 |
set_seed |
string; random numbers to initiate starting position. e.g. "79151 17351". Can be left blank and a seed will be generated. |
ignore_missing |
logical; Should sda ignore samples with completely missing data. |
remove_zero_comps |
logical; should components with all PIPs < 0.05 be removed |
eigen_parallel |
logical; use multi-threading options in eigen. |
num_blocks |
int; number of blocks to split loadings matrix into for parallel updates. |
num_openmp_threads |
int; number of threads to use in parallel mode |
save_everything |
logical; if true will save all parameter estimated including for example noise precision. |
debug |
logical; if true will calculate free energy at every iteration (slower) |
run_SDA
Run SDA
Nothing, the results are saved on disk in the directory specified in the parameter 'out'.
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