LFQbench.changeConfiguration: LFQbench.changeConfiguration
In IFIproteomics/LFQbench: Label Free Quantitation benchmark package

LFQbench.changeConfiguration

R Documentation

LFQbench.changeConfiguration

Description

change some of the initialized LFQbench configuration settings. LFQbench.changeConfiguration allows to change some configuration settings without loading default values.

Usage

LFQbench.changeConfiguration(DataRootFolder = LFQbench.Config$DataRootFolder,
  SampleComposition = LFQbench.Config$SampleComposition,
  BackgroundSpeciesName = LFQbench.Config$BackgroundSpeciesName,
  InputExtensionPattern = LFQbench.Config$InputExtensionPattern,
  CsvColumnSeparator = LFQbench.Config$CsvColumnSeparator,
  CsvDecimalPointChar = LFQbench.Config$CsvDecimalPointChar,
  BoxPlotWhiskerQuantile = LFQbench.Config$BoxPlotWhiskerQuantile,
  MinProteinAmount = LFQbench.Config$MinProteinAmount,
  DropInvalidLogRatio = LFQbench.Config$DropInvalidLogRatio,
  LogRatioValidityRangeSDFactor = LFQbench.Config$LogRatioValidityRangeSDFactor,
  LogRatioPlotRange = LFQbench.Config$LogRatioPlotRange,
  LogIntensityPlotRange = LFQbench.Config$LogIntensityPlotRange,
  MaxLogRatioForAUQC = LFQbench.Config$MaxLogRatioForAUQC,
  NumberOfIntensityQuantiles = LFQbench.Config$NumberOfIntensityQuantiles,
  CenterLogRatioByBackground = LFQbench.Config$CenterLogRatioByBackground,
  NormalizeAmountsToPPM = LFQbench.Config$NormalizeAmountsToPPM,
  PlotWidth = LFQbench.Config$PlotWidth,
  PlotHeight = LFQbench.Config$PlotHeight,
  PlotCurveLineWidth = LFQbench.Config$PlotCurveLineWidth,
  PlotLegendLineWidth = LFQbench.Config$PlotLegendLineWidth,
  PlotPointSize = LFQbench.Config$PlotPointSize,
  ScatterPlotPointType = LFQbench.Config$ScatterPlotPointType,
  ScatterPlotPointMinAlpha = LFQbench.Config$ScatterPlotPointMinAlpha,
  ScatterPlotLowessBandWidth = LFQbench.Config$ScatterPlotLowessBandWidth,
  AxisLabelSize = LFQbench.Config$AxisLabelSize,
  AxisAnnotationSize = LFQbench.Config$AxisAnnotationSize,
  AxisLineThickness = LFQbench.Config$AxisLineThickness,
  AxisXLabelNumDiv = LFQbench.Config$AxisXLabelNumDiv,
  AxisYLabelNumDiv = LFQbench.Config$AxisYLabelNumDiv,
  par = LFQbench.Config$par)

Arguments

`DataRootFolder`	the parent folder for batch processing
`SampleComposition`	the quantitative composition of hybrid proteome samples
`BackgroundSpeciesName`	the name of non regulated background species
`InputExtensionPattern`	the pattern of file extension for batch input files
`CsvColumnSeparator`	the input file column delimiter character
`CsvDecimalPointChar`	the input file decimal point character
`BoxPlotWhiskerQuantile`	the quantile to that whiskers of boxplots will extend, t.m. (1 - quantile*2) portion of data will be inside the whiskers
`MinProteinAmount`	the minimum valid protein amount in the input data, protein amounts below this threshold are considered as NA
`DropInvalidLogRatio`	if TRUE log-ratios outside validity range will be dropped
`LogRatioValidityRangeSDFactor`	validity range is calculated as mean +/- SD * SDFactor (separately for each species)
`LogRatioPlotRange`	the log-ratio range for plotting
`LogIntensityPlotRange`	the log2-intensity range for plotting
`MaxLogRatioForAUQC`	the maximum value for AUQC quantification
`NumberOfIntensityQuantiles`	the log2-intensity ranges for range based plots
`CenterLogRatioByBackground`	should we center all log-ratios by the median log-ratio of the background species
`NormalizeAmountsToPPM`	should we normalize amounts to ppms
`PlotWidth`	the plot width in inches used in pdf files
`PlotHeight`	the plot height in inches used in pdf files
`PlotCurveLineWidth`	the line thickness for curves in plots
`PlotLegendLineWidth`	the line thickness in legends
`PlotPointSize`	the point size
`ScatterPlotPointType`	the point type
`ScatterPlotPointMinAlpha`	the minimum alpha value used for coloring points in sparse regions
`ScatterPlotLowessBandWidth`	the lowess locality parameter f, use values (local) 0 < f <= 1 (global)
`AxisLabelSize`	the relative font size for axis labels
`AxisAnnotationSize`	the relative font size for axis labels
`AxisLineThickness`	the line thickness of axes
`par`	the graphical parameters like mar, mgp, las, ... to set for the plot canvases.