# Calibration curves for targeted proteomics, lipidomics and metabolomics data

## 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).