Package 'rawDiag'

Title: Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Description: Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.
Authors: Christian Panse [aut, cre] , Christian Trachsel [aut], Tobias Kockmann [aut]
Maintainer: Christian Panse <[email protected]>
License: GPL-3
Version: 1.3.4
Built: 2024-11-13 03:24:44 UTC
Source: https://github.com/bioc/rawDiag

Help Index

Calculate Master Scan Number

Description

calculates the MS1 master scan number of an MS2 scan and populates the MasterScanNumber with it

Usage

.calculatioMasterScan(x)

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.

Value

a data.frame containing a MasterScanNumber column.

Author(s)

Christian Trachsel

Calculate MS Cycle Time

Description

calculates the lock mass deviations along RT.

Usage

.cycleTime(x)

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.

Value

calculates the time of all ms cycles and the 95 the cycle time is defined as the time between two consecutive MS1 scans

Note

TODO: quantile part needed? If no MS1 scan is present? E.g., DIA take lowest window as cycle indicator?

Author(s)

Christian Trachsel (2017), Christian Panse (20231201) refactored

Fill NA values with last previous value

Description

Fill NA values with last previous value

Usage

.fillNAgaps(x)

Arguments

x

a vector of values

Value

a vector with any NA values replaced with the last previous actuall value

Author(s)

Christian Trachsel

Examples

c(NA, 1, 2, 3, NA, 4, 5, NA, NA, NA, 6) |>
  rawDiag:::.fillNAgaps()

Build the rawDiag shiny application

Description

Build the rawDiag shiny application

Usage

buildRawDiagShinyApp(rawDir = (dirname(rawrr::sampleFilePath())))

Arguments

rawDir

A directory containing the input raw files, default is set to the $HOME/Downloads directory.

Value

returns the rawDiag shiny apps

Note

launch the shiny application by embracing your command line while expecting the raw file in $HOME/Downloads

  • MacOSX and Linux: ⁠R -q -e "library(rawDiag); buildRawDiagShinyApp() |> shiny::runApp(launch.browser = TRUE)"⁠

  • Microsoft Windows: ⁠R.exe -e "library(rawDiag); buildRawDiagShinyApp() |> shiny::runApp(launch.browser = TRUE)"⁠

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |>
  dirname() |>
  rawDiag::buildRawDiagShinyApp() |>
  shiny::runApp()
  
 # or use your 'Download' folder
 (Sys.getenv('HOME') |>
   file.path("Downloads")) |>
   rawDiag::buildRawDiagShinyApp() |>
   shiny::runApp()

Checks Bioconductor installation instructions

Description

Checks Bioconductor installation instructions

Usage

checkRawrr()

Value

TRUE if everything is installed correctly

Is an Object an rawDiag Object?

Description

Is an Object an rawDiag Object?

Usage

is.rawDiag(object)

Arguments

object

any R object.

Value

a boolean

Author(s)

Christian Panse 2018

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::is.rawDiag()

Charge State Overview Plot

Description

graphs the number of occurrences of all selected precursor charge states.

Usage

plotChargeState(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() -> S
 S |> rawDiag::plotLockMassCorrection()

Cycle Load Plot

Description

plotting the number of MS2 per MS1 (the duty cycle) scan versus retention time. The deepskyblue colored loess curve shows the trend.

Usage

plotCycleLoad(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() -> S

S |> rawDiag::plotCycleLoad()

Plot Cycle Time

Description

graphs the time difference between two consecutive MS1 scans (cycle time) with respect to RT (scatter plots) or its density (violin). A smooth curve graphs the trend. The 95th percentile is indicated by a red dashed line.

Usage

plotCycleTime(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::plotCycleTime()

Plot Injection Time

Description

shows the injection time density of each mass spectrometry file as a violin plot. The higher the maximum number of MS2 scans is in the method, the more the density is shifted towards the maximum injection time value.

Usage

plotInjectionTime(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::plotInjectionTime()

Lock Mass Correction Plot

Description

Lock Mass Correction Plot

Usage

plotLockMassCorrection(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |>
  rawDiag::readRaw() |>
  rawDiag::plotLockMassCorrection()

Mass Distribution Plot

Description

plots the mass frequency in dependency to the charge state

Usage

plotMassDistribution(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Details

displays charge state resolved frequency of precursor masses.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::plotMassDistribution('overlay')

mZ Distribution Plot of Ms2 Scans

Description

draws precursor mass vs retention time for each MS2 scan in the raw file.

Usage

plotMzDistribution(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() -> S
rawDiag::plotMzDistribution(S)

Precursor Mass versus StartTime MS2 based hexagons

Description

Precursor Mass versus StartTime MS2 based hexagons

Usage

plotPrecursorHeatmap(x, method = "overlay", bins = 80)

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.
bins

number of bins in both vertical and horizontal directions. default is 80.

Value

a ggplot object.

Note

TODO: define bin with dynamically as h= 2x IQR x n e-1/3 or number of bins (max-min)/h

Author(s)

Christian Trachsel (2017)

References

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::plotPrecursorHeatmap()

Scan Event Plot

Description

Plotting the elapsed scan time for each individual scan event.

Usage

plotScanTime(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot object.

Author(s)

Christian Trachsel (2017), Christian Panse (2023)

References

Examples

## for debugging bioconductor check
 if (Sys.info()['sysname'] %in% c("Darwin", "Linux")) {Sys.which('mono')}
 rawrr::sampleFilePath() |> rawDiag::readRaw() -> S

rawDiag::checkRawrr()

S |> rawDiag::plotScanTime()

Total Ion Count and Base Peak Plot

Description

displays the Total Ion Count (TIC) and the Base Peak Chromatogram of a mass spectrometry measurement. Multiple files are handled by faceting based on rawfile name.

Usage

plotTicBasepeak(x, method = "trellis")

Arguments

x

a data.frame object adhering to the specified criteria for the is.rawDiag function.
method

specifying the plot method 'trellis' | 'violin' | 'overlay'. The default is 'trellis'.

Value

a ggplot2 object for graphing the TIC and the Base Peak chromatogram.

Author(s)

Christian Trachsel (2017), Christian Panse (20231130) refactored

Examples

rawrr::sampleFilePath() |> rawDiag::readRaw() |> rawDiag::plotTicBasepeak()

rawDiag shiny module

Description

rawDiag shiny module

Usage

rawDiagServer(id, vals)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.
vals

containing rawfile

Value

rawDiag shiny module server

Examples

shiny::shiny(rawDir = (rawrr::sampleFilePath() |> dirname()))

rawDiag shiny module UI

Description

rawDiag shiny module UI

Usage

rawDiagUI(id)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

Value

a shiny UI module

rawDiag shiny module UI

Examples

rawDiag::shiny(rawDir = (rawrr::sampleFilePath() |> dirname()))

Reads selected raw file trailer information for rawDiag plot functions

Description

implements a wrapper function using the rawrr methods readIndex, readTrailer, and readChromatogram to read proprietary mass spectrometer generated data using third-party libraries.

Usage

readRaw(
  rawfile,
  msgFUN = function(x) {
     message(x)
 }
)

Arguments

rawfile

the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
msgFUN

this function is used for logging information while composing the resulting data.frame. It can also be used for shiny progress bar. The default is using the message.

Value

a data.frame containing the selected trailer information.

Note

The set up procedure for the rawrr package needs to be run in order to use this package.

Author(s)

Christian Panse (2016-2023)

References

doi:10.1021/acs.jproteome.8b00173

Examples

rawDiag::checkRawrr()
rawrr::sampleFilePath() |>
  rawDiag::readRaw()