These options are best set via orbi_options()
and queried via orbi_get_option()
. However, the base functions options()
and getOption()
work as well but require an isoorbi.
prefix (the package name and a dot) for the option name. Setting an option to a value of NULL
means that the default is used. orbi_get_options()
is available as an additional convenience function to retrieve a subset of options with a regular expression pattern.
Arguments
- ...
set package options, syntax identical to
options()
- pattern
to retrieve multiple options (as a list) with a shared pattern
- x
name of the specific option to retrieve
Functions
orbi_options()
: set/get option valuesorbi_get_options()
: get a subset of option values that fit a patternorbi_get_option()
: retrieve the current value of one option (option must be defined for the package)
Options for the isoorbi package
di_ref_name
: the text label for dual inlet reference blocksdi_sample_name
: the text label for dual inlet sample blocksdata_type_data
: the text used to flag raw data as actually being datadata_type_startup
: the text used to flag raw data as being part of the startupdata_type_changeover
: the text used to flag raw data as being part of a changeoverdata_type_unused
: the text used to flag raw data as being unusedinclude_spectra
: whether to include the spectral data in orbi_read_raw.raw_aggregator
: configuration for pulling data out of raw filesdebug
: turn on debug mode
Examples
# All default options
orbi_get_options()
#> $di_ref_name
#> [1] "ref"
#>
#> $di_sample_name
#> [1] "sam"
#>
#> $data_type_data
#> [1] "data"
#>
#> $data_type_startup
#> [1] "startup"
#>
#> $data_type_changeover
#> [1] "changeover"
#>
#> $data_type_unused
#> [1] "unused"
#>
#> $include_spectra
#> [1] FALSE
#>
#> $raw_aggregator
#> # A tibble: 22 × 8
#> dataset column source default regexp cast func args
#> <chr> <chr> <list> <lgl> <lgl> <chr> <chr> <list>
#> 1 file_info "uid" <list [1]> NA FALSE as.fact… NA <NULL>
#> 2 file_info "\\1" <list [1]> NA TRUE as.char… NA <NULL>
#> 3 scans "scan" <list [1]> NA FALSE as.inte… NA <NULL>
#> 4 scans "time.min" <list [1]> NA FALSE as.nume… NA <NULL>
#> 5 scans "tic" <list [1]> NA FALSE as.nume… NA <NULL>
#> 6 scans "it.ms" <list [1]> NA FALSE as.nume… NA <NULL>
#> 7 scans "resolution" <list [1]> NA FALSE as.nume… NA <NULL>
#> 8 scans "basePeakIntensity" <list [1]> NA FALSE as.nume… sapp… <list>
#> 9 scans "rawOvFtT" <list [1]> NA FALSE as.nume… NA <NULL>
#> 10 scans "intensCompFactor" <list [1]> NA FALSE as.nume… NA <NULL>
#> # ℹ 12 more rows
#>
#> $debug
#> [1] FALSE
#>
# Options that contain 'data' in the name
orbi_get_options("data")
#> $data_type_data
#> [1] "data"
#>
#> $data_type_startup
#> [1] "startup"
#>
#> $data_type_changeover
#> [1] "changeover"
#>
#> $data_type_unused
#> [1] "unused"
#>
# Specific option
orbi_get_option("data_type_unused")
#> [1] "unused"
# Change an option
orbi_options(data_type_unused = "flagged")
orbi_get_option("data_type_unused")
#> [1] "flagged"
# Change back to default
orbi_options(data_type_unused = NULL)
orbi_get_option("data_type_unused")
#> [1] "unused"