Package options — orbi_options • isoorbi

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.

Usage

orbi_options(...)

orbi_get_options(pattern = NULL)

orbi_get_option(x)

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 values
orbi_get_options(): get a subset of option values that fit a pattern
orbi_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 blocks
di_sample_name: the text label for dual inlet sample blocks
data_type_data: the text used to flag raw data as actually being data
data_type_startup: the text used to flag raw data as being part of the startup
data_type_changeover: the text used to flag raw data as being part of a changeover
data_type_unused: the text used to flag raw data as being unused
aggregators: data aggregators for pulling data out of raw files. The list of available aggregators is accessible via orbi_get_option("aggregators"). Individiual aggregators are available via the shortcut helper function orbi_get_aggregator("standard"). Register new/overwrite existing aggregators via orbi_register_aggregator().
debug: turn on debug mode
auto_use_ansi: whether to automatically enable correct rendering of stylized (ansi) output in HTML reports from notebooks that call library(isoorbi). Can be turned off by calling isoorbi::orbi_options(auto_use_ansi = FALSE) before call library(isoorbi).

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"
#> 
#> $aggregators
#> $aggregators$minimal
#> ────────────────────────────── Aggregator minimal ──────────────────────────────
#> Dataset file_info:
#>  → filename = as.character(sub(FileName, pattern = ".raw", replacement = "",
#> fixed = TRUE))
#>  → creation_date = as.POSIXct(CreationDate)
#>  → in_aquisition = as.logical(InAquisition)
#> Dataset scans:
#>  → scan.no = as.integer(scan.no)
#>  → time.min = as.numeric(StartTime)
#>  → tic = as.numeric(TIC)
#>  → it.ms = as.numeric(`Ion Injection Time (ms)`)
#>  → resolution = as.numeric(one_of(`FT Resolution`, `Orbitrap Resolution`))
#>  → microscans = as.integer(`Micro Scan Count`)
#> Dataset peaks:
#>  → scan.no = as.integer(scan.no)
#>  → mzMeasured = as.numeric(mass)
#>  → intensity = as.numeric(intensity)
#>  → baseline = as.numeric(baseline)
#>  → peakNoise = as.numeric(noise)
#>  → peakResolution = as.numeric(resolution)
#>  → isRefPeak = as.logical(is_ref)
#>  → isLockPeak = as.logical(is_lock_peak)
#> Dataset spectra:
#>  → scan.no = as.integer(scan.no)
#>  → mz = as.numeric(mass)
#>  → intensity = as.numeric(intensity)
#> 
#> $aggregators$standard
#> ────────────────────────────── Aggregator standard ─────────────────────────────
#> Dataset file_info:
#>  → filename = as.character(sub(FileName, pattern = ".raw", replacement = "",
#> fixed = TRUE))
#>  → creation_date = as.POSIXct(CreationDate)
#>  → in_aquisition = as.logical(InAquisition)
#>  → (.*) = as.character(all_matches("(.*)"))
#> Dataset scans:
#>  → scan.no = as.integer(scan.no)
#>  → time.min = as.numeric(StartTime)
#>  → tic = as.numeric(TIC)
#>  → it.ms = as.numeric(`Ion Injection Time (ms)`)
#>  → resolution = as.numeric(one_of(`FT Resolution`, `Orbitrap Resolution`))
#>  → microscans = as.integer(`Micro Scan Count`)
#>  → basePeakMz = as.numeric(BasePeakMass)
#>  → basePeakIntensity = as.numeric(BasePeakIntensity)
#>  → lowMass = as.numeric(LowMass)
#>  → highMass = as.numeric(HighMass)
#>  → rawOvFtT = as.numeric(RawOvFtT)
#>  → intensCompFactor = as.numeric(`OT Intens Comp Factor`)
#>  → agc = as.character(AGC)
#>  → agcTarget = as.integer(`AGC Target`)
#>  → numberLockmassesFound = as.integer(`Number of LM Found`)
#>  → analyzerTemperature = as.numeric(`Analyzer Temperature`)
#> Dataset peaks:
#>  → scan.no = as.integer(scan.no)
#>  → mzMeasured = as.numeric(mass)
#>  → intensity = as.numeric(intensity)
#>  → baseline = as.numeric(baseline)
#>  → peakNoise = as.numeric(noise)
#>  → peakResolution = as.numeric(resolution)
#>  → isRefPeak = as.logical(is_ref)
#>  → isLockPeak = as.logical(is_lock_peak)
#> Dataset spectra:
#>  → scan.no = as.integer(scan.no)
#>  → mz = as.numeric(mass)
#>  → intensity = as.numeric(intensity)
#> 
#> $aggregators$extended
#> ────────────────────────────── Aggregator extended ─────────────────────────────
#> Dataset file_info:
#>  → filename = as.character(sub(FileName, pattern = ".raw", replacement = "",
#> fixed = TRUE))
#>  → creation_date = as.POSIXct(CreationDate)
#>  → in_aquisition = as.logical(InAquisition)
#>  → (.*) = as.character(all_matches("(.*)"))
#> Dataset scans:
#>  → scan.no = as.integer(scan.no)
#>  → time.min = as.numeric(StartTime)
#>  → tic = as.numeric(TIC)
#>  → it.ms = as.numeric(`Ion Injection Time (ms)`)
#>  → resolution = as.numeric(one_of(`FT Resolution`, `Orbitrap Resolution`))
#>  → microscans = as.integer(`Micro Scan Count`)
#>  → basePeakMz = as.numeric(BasePeakMass)
#>  → basePeakIntensity = as.numeric(BasePeakIntensity)
#>  → lowMass = as.numeric(LowMass)
#>  → highMass = as.numeric(HighMass)
#>  → rawOvFtT = as.numeric(RawOvFtT)
#>  → intensCompFactor = as.numeric(`OT Intens Comp Factor`)
#>  → agc = as.character(AGC)
#>  → agcTarget = as.integer(`AGC Target`)
#>  → numberLockmassesFound = as.integer(`Number of LM Found`)
#>  → analyzerTemperature = as.numeric(`Analyzer Temperature`)
#>  → (.*) = as.character(all_matches("(.*)"))
#> Dataset peaks:
#>  → scan.no = as.integer(scan.no)
#>  → mzMeasured = as.numeric(mass)
#>  → intensity = as.numeric(intensity)
#>  → baseline = as.numeric(baseline)
#>  → peakNoise = as.numeric(noise)
#>  → peakResolution = as.numeric(resolution)
#>  → isRefPeak = as.logical(is_ref)
#>  → isLockPeak = as.logical(is_lock_peak)
#> Dataset spectra:
#>  → scan.no = as.integer(scan.no)
#>  → mz = as.numeric(mass)
#>  → intensity = as.numeric(intensity)
#> 
#> 
#> $debug
#> [1] FALSE
#> 
#> $auto_use_ansi
#> [1] TRUE
#> 

# 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"