run_SDA: run_SDA

In marchinilab/SDAtools: SDAtools: A toolkit for SDA

Description

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.

Usage

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)

Arguments

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)

Details

run_SDA Run SDA

Value

Nothing, the results are saved on disk in the directory specified in the parameter 'out'.

marchinilab/SDAtools documentation built on Jan. 31, 2020, 3:51 a.m.