View source: R/load_input_and_run_cape.R
load_input_and_run_cape | R Documentation |
This function loads the input file path and runs cape It is used to run CAPE from a non R script (python)
load_input_and_run_cape( input_file = NULL, yaml_params = NULL, results_path = NULL, run_parallel = FALSE, results_file = "cross.RDS", p_or_q = 0.05, n_cores = 4, initialize_only = FALSE, verbose = TRUE, param_file = NULL, create_report = FALSE, qtl_id_col = NULL, qtl_na_strings = "-" )
input_file |
data input to be loaded |
yaml_params |
a parameter set up in the form of a YAML string |
results_path |
path to the results |
run_parallel |
boolean, if TRUE runs certain parts of the code as parallel blocks |
results_file |
the name of the saved data_obj RDS file. The base name is used as the base name for all saved RDS files. |
p_or_q |
A threshold indicating the maximum adjusted p value considered |
n_cores |
integer, default is 4 |
initialize_only |
boolean, default: FALSE |
verbose |
boolean, output goes to stdout |
param_file |
path to yml parameter file for running cape |
create_report |
boolean, if true we create the corresponding HTML report page |
qtl_id_col |
argument for read_population, an optional column number for individual IDs |
qtl_na_strings |
argument for read_population, an optional string for missing values |
## Not run: #load input in qtl2 zip format load_input_and_run_cape("cross_file.zip") #load input in qtl csv format load_input_and_run_cape("cross_file.csv") ## End(Not run)
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