Filtering_datasets      Filtering tools for Galaxy scripting
W4MLogger               The W4MLogger Class
W4MLogger_.message__    W4MLogger_.message__
W4MLogger_[info,warning,error,debug,verbose]
                        Log info/warning/error/debug/verbose messages
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
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_param_type_n_length
                        check_param_type_n_length - to check parameters
check_parameter_length
                        check_parameter_length - validate parameter's
                        length
check_parameter_type    check_parameter_type - validate parameter's
                        type
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.
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
in_galaxy_env           in_galaxy_env - check if the script has been
                        run by galaxy
intens_check            Checking intensities of a data set following
                        the W4M 3-tables format
intensity_checks        Intensity checking tools for Galaxy scripting
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
