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

LFQbench.initConfiguration

R Documentation

LFQbench.initConfiguration

Description

Initialization of LFQbench configuration settings. Executing the function without parameters will use default values. Use function LFQbench.changeConfiguration to change settings after initialization.

Usage

LFQbench.initConfiguration(DataRootFolder = getwd(),
  SampleComposition = data.frame(species = c("HUMAN", "YEAST", "ECOLI"), A =
  c(65, 30, 5), B = c(65, 15, 20)), BackgroundSpeciesName = "HUMAN",
  InputExtensionPattern = "\\..sv$", CsvColumnSeparator = "\t",
  CsvDecimalPointChar = ".", BoxPlotWhiskerQuantile = 0.025,
  MinProteinAmount = 1e-06, DropInvalidLogRatio = T,
  LogRatioValidityRangeSDFactor = 5, LogRatioPlotRange = c(-4, 4),
  LogIntensityPlotRange = NULL, MaxLogRatioForAUQC = 2,
  NumberOfIntensityQuantiles = 3, CenterLogRatioByBackground = T,
  NormalizeAmountsToPPM = F, PlotWidth = 6, PlotHeight = 5,
  PlotCurveLineWidth = 2, PlotLegendLineWidth = 4, PlotPointSize = 1.5,
  ScatterPlotPointType = 20, ScatterPlotPointMinAlpha = 0.5,
  ScatterPlotLowessBandWidth = 0.8, AxisLabelSize = 2,
  AxisAnnotationSize = 2, AxisLineThickness = 2, AxisXLabelNumDiv = NULL,
  AxisYLabelNumDiv = NULL, par = list(mar = c(4.5, 6, 0.5, 0.5), mgp =
  c(3.7, 1.5, 0), las = 1))

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 number of parts for splitting the data for metrics calculation
`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
`AxisXLabelNumDiv`	divide the number of labels displayed in axis X
`AxisYLabelNumDiv`	divide the number of labels displayed in axis Y
`par`	the graphical parameters like mar, mgp, las, ... to set for the plot canvases.