Function reference • midar

All functions

MidarExperiment-class: S4 Class Representing the MIDAR Dataset

MidarExperiment(): Constructor for the MidarExperiment object.

add_lipid_class_transition(): Retrieve lipid name, lipid class and transition from feauture names

analysis_type(<MidarExperiment>): Get analysis_type

`analysis_type<-`(<MidarExperiment>): Set analysis_type

`analysis_type<-`(): Get analysis type

analysis_type(): Set analysis type

apply_qc_filter(): Filter dataset according to QC and other criteria

calculate_qc_metrics(): Calculate QC metrics for each feature

`$`(<MidarExperiment>): Getter for specific slots of an MidarExperiments object

combine_experiments(): Combines a list of MidarExperiments into one

corr_batch_centering(): Batch centering

corr_drift_fun(): Drift Correction by Custom Function

corr_drift_gaussiankernel(): Drift Correction by Gaussian Kernel Smoothing

corr_drift_loess(): Drift Correction by LOESS Smoothing

correct_interference_manually(): Manual correction for interference contributed by another feature

correct_interferences(): Substract interferences contributed by another feature

cvlog(): Coefficient of variation (CV) using log-transformed data

exportWideCSV(): Export any parameter to a wide-format table

fun_gaussiankernel(): Gaussian Kernel smoothing helper function

fun_loess(): Loess smoothing helper function

get_stats(): Get FC and p values from a t test contrast

import_masshunter_csv(): Read and convert an Agilent MassHunter Quant CSV result file

import_masshunter_csv_wide(): Reads a wide CSV file with Feature Intensities

import_msorganizer_xlm(): Imports metadata provided by an MSOrganizer EXCEL template

normalize_by_istd(): Normalize Intensities with corresponding ISTD Intensities

plot_pca_qc(): PCA plot for QC

plot_responsecurves(): Response curves plot

plot_runscatter(): RunScatter plot

plot_x_vs_y(): Plot comparison of analytical CV before and after ISTD-normalization

quantitate_by_istd(): Quantitate using sample and spiked ISTD amounts

read_MRMkit_raw_area_CSV(): Read and convert an Agilent MassHunter Quant CSV result file

read_MRMkit_results(): Reads a long CSV file with Feature Intensities

read_long_table_csv(): Reads a long CSV file with Feature Intensities

read_masshunter_csv(): Reads an Agilent MassHunter Quant CSV file

read_msorganizer_xlm(): Import metadata from the MSOrganizer template (.XLM)

read_table_wide(): Reads a wide CSV or XLSX sheet with Feature Values

saveQCinfo(): Save the QC table to a CSV file

volcano_plot(): Get FC and p values from a t test contrast

writeReportXLS(): Writes all a data processing report to an EXCEL file