R: Useful Functions for Harmonized W4M Tool Development

# Useful Functions for Harmonized W4M Tool Development

## Documentation for package ‘W4MRUtils’ version 1.2.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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.
Filtering_datasets | Filtering tools for Galaxy scripting
generic_filter | Filtering a data set following the 3-tables format
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
intensity_checks | Intensity checking tools for Galaxy scripting
intens_check | Checking intensities of a data set following the W4M 3-tables format
in_galaxy_env | in_galaxy_env - check if the script has been run by galaxy
match2 | Table match check functions
match3 | match3
metab_merge | Merging a dataMatrix with a metadata file
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