# Quantitative Metabolomics Data Processing Tools

## Documentation for package ‘qmtools’ version 1.4.0

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

## Help Pages

clusterFeatures | Feature clustering
compareSamples | Sample comparison
faahko_se | FAAH knockout LC/MS data SummarizedExperiment
imputeIntensity | Imputation methods
imputeIntensity-method | Imputation methods
imputeKNN | k-nearest neighbor imputation
normalizeIntensity | Normalization methods
normalizeIntensity-method | Normalization methods
normalizePQN | Probabilistic quotient normalization (PQN)
plotBox | Box plot
plotCorr | Correlation plot
plotMiss | Missing value plot
plotReduced | Score plot of dimension-reduced data
plotRTgroup | Helper to visualize feature grouping
reduceFeatures | Dimension reduction methods
reduceFeatures-method | Dimension reduction methods
reducePCA | Principal component analysis (PCA)
reducePLSDA | Partial least squares-discriminant analysis (PLS-DA)
reduceTSNE | t-distributed stochastic neighbor embedding (t-SNE)
removeBlankRatio | Feature Filtering based on QC/blank ratio
removeFeatures | Feature Filtering methods
removeFeatures-method | Feature Filtering methods
removeICC | Feature Filtering based on ICC
removeMiss | Feature filtering based on proportions of missing values
removeRSD | Feature Filtering based on RSD
scaleCols | Scale along columns (samples)
scaleRows | Scale along rows (features)