Calibration curves for targeted proteomics, lipidomics and metabolomics data

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Documentation for package ‘CalibraCurve’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.calcContPrelimRanges	PLR: Calculate key features for the existing continuous preliminary ranges
.calcCV	PLR: calculate CV for one concentration level
.calcLinearModel	FLR: calculate weighted or unweighted linear model
.calcPerBias	FLR: calculate percent bias for a specific concentration level
.calcPerBiasAvgSDCV	FLR: calculate average, SD and CV percent bias for each concentration level
.calcPerBiasLevels	FLR: calculate list of percent bias values for all concentration levels
.calcResponseFactors	Calculate Response factors
.calcWeights	FLR: calculate weights for linear model for a specific concentration level
.checkFinalRange	FLR: checks if final linear range has been reached (compare average percent bias with threshold)
.checkNumberReplicates	Data preprocessing: Helper function to check for sufficient number of replicates for a specific concentration level
.filterConcentrationLevel	Data preprocessing: Helper function to select all rows from a specific concentration level
.prepareAnnotationData	Prepare annotation data
.prepareCalibData	Prepare calibration data
.prepareCurveData	Prepare curve data
.saveCCResult	Save results of CalibraCurve
.saveTablesAndPlots	Save result tables and plots
.selctConcLevel	FLR: selects the highest or lowest concentration level for removal
assemble_results	Assemble result tables
calcRF	Calculate Response factors
calculate_FLR	Calculate the final linear range
calculate_PLR	Calculate preliminary linear range (PLR)
calc_single_curve	Calculate all necessary steps for a single calibration curve
CalibraCurve	CalibraCurve
cleanData	Clean data (remove 0s and NAs, remove concentration levels with insufficient number of replicates)
plotCalibraCurve	Plot the calibration curve
plotResponseFactors	Plot response factors
predictConcentration	Predict concentrations from intensity values based on a given calibration curve
readDataSE	Read data stored as an SummarizedExperiment object (directly or stored in an .rds file). Extracts the two relevant columns (concentration and measurement) and orders the data by increasing concentration level.
readDataTable	Read data in different table input formats (xlsx, csv or txt). Extracts the two relevant columns (concentration and measurement) and orders the data by increasing concentration.
readMultipleTables	Read folder of files in different table input formats (xlsx, csv or txt).