Utils List for W4M - Workflow for Metabolomics
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Documentation for package ‘W4MRUtils’ version 1.0.0
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| check_err | Check Errors |
| check_one_character | check_one_character |
| check_one_complex | check_one_complex |
| check_one_integer | check_one_integer |
| check_one_logical | check_one_logical |
| check_one_numeric | check_one_numeric |
| check_parameter_length | check_parameter_length - validate parameter's length |
| check_parameter_type | check_parameter_type - validate parameter's type |
| check_param_type_n_length | check_param_type_n_length - to check parameters |
| collapse | collapse - to paste strings with collapse = "" |
| collapse_lines | collapse_lines - to paste strings with collapse = "\n" |
| convert_parameters | Convert Parameters |
| df_force_numeric | Convert data frame to numeric. |
| df_is | Test type of a data frame. |
| df_read_table | Data frame loading from a file. |
| get_base_dir | get_base_dir - to get... the base directory |
| get_logger | Instantiate a Logger |
| get_r_env | get_r_env - provides env vars begining with R_* |
| import2 | Import two W4M tables |
| import3 | Import the three W4M tables |
| in_galaxy_env | in_galaxy_env - check if the script has been run by galaxy |
| match2 | Table match check functions |
| match3 | match3 |
| mini_tools | Mini tools for Galaxy scripting |
| optparse_character | optparse_character - define a command parameter as string |
| optparse_flag | optparse_flag - define a command parameter as a trigger |
| optparse_integer | optparse_integer - define a command parameter as an integer |
| optparse_list | optparse_list - define a command parameter as a list of objects |
| optparse_numeric | optparse_numeric - define a command parameter as an numeric |
| optparse_parameters | optparse_parameters - parse easily the command line parameters |
| parse_args | Parse Command arguments |
| printf | printf - to format a string and print it |
| printfp | printfp - to paste, format and print a string |
| printp | printp - to format a string and print it |
| reproduce_id | Reproduce ID |
| run_galaxy_function | run_galaxy_function - automate running functions in galaxy |
| run_galaxy_processing | run_galaxy_processing - automate running code in galaxy |
| show_galaxy_footer | show_galaxy_footer - shows the footer for glaxy tools |
| show_galaxy_header | show_galaxy_header - shows the header for glaxy tools |
| show_sys | show_sys - prints env variables related to R |
| shy_lib | Shy Lib |
| source_local | source_local - source file, from absolute or relative path |
| stock_id | Stock ID |
| stopaste | stopaste - to paste string to a message and stop |
| stopaste0 | stopaste0 - to paste string to a message and stop |
| stopf | stopf - to stop and format message |
| unmangle_galaxy_param | unmangle_galaxy_param - revert effects of galaxy manglings. |
| unmangle_galaxy_string | unmangle_galaxy_string - revert effects of galaxy mangling |
| W4MLogger | The W4MLogger Class |
| W4MLogger$debug | Log info/warning/error/debug/verbose messages |
| W4MLogger$error | Log info/warning/error/debug/verbose messages |
| W4MLogger$info | Log info/warning/error/debug/verbose messages |
| W4MLogger$verbose | Log info/warning/error/debug/verbose messages |
| W4MLogger$warning | Log info/warning/error/debug/verbose messages |
| W4MLogger_.message__ | W4MLogger_.message__ |
| W4MLogger_add_out_paths | Adds a file where logs are duplicated |
| W4MLogger_finalize | W4MLogger_finalize |
| W4MLogger_set_debug | W4MLogger$set_debug |
| W4MLogger_set_error | W4MLogger$set_error |
| W4MLogger_set_info | W4MLogger$set_info |
| W4MLogger_set_out_paths | Defines in which file logs are duplicated |
| W4MLogger_set_verbose | W4MLogger$set_verbose |
| W4MLogger_set_warning | W4MLogger$set_warning |
| W4MLogger_[info,warning,error,debug,verbose] | Log info/warning/error/debug/verbose messages |