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