R: Core Utils for Mass Spectrometry Data

# Core Utils for Mass Spectrometry Data

## Documentation for package ‘MsCoreUtils’ version 1.24.0

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

## Help Pages

%between% | Range helper functions
aggregate | Aggreagate quantitative features
aggregate_by_matrix | Aggreagate quantitative features
aggregate_by_vector | Aggreagate quantitative features
asInteger | Coerce functions
between | Range helper functions
bin | Binning
breaks_ppm | Sequence with increasing difference between elements
closest | Relaxed Value Matching
coefMA | Smoothing
coefSG | Smoothing
coefWMA | Smoothing
coerce | Coerce functions
colCounts | Counts the number of features
colMeansMat | Aggreagate quantitative features
colSumsMat | Aggreagate quantitative features
common | Relaxed Value Matching
common_path | Extract the common file path
distance | Spectra Distance/Similarity Measurements
dotproduct | Spectra Distance/Similarity Measurements
entropy | Spectral entropy
estimateBaseline | Estimates the Baseline of a Mass Spectrum
estimateBaselineConvexHull | Estimates the Baseline of a Mass Spectrum
estimateBaselineMedian | Estimates the Baseline of a Mass Spectrum
estimateBaselineSnip | Estimates the Baseline of a Mass Spectrum
estimateBaselineTopHat | Estimates the Baseline of a Mass Spectrum
force_sorted | Forcing a numeric vector into a monotonously increasing sequence.
formatRt | Format Retention Time
getImputeMargin | Quantitative mass spectrometry data imputation
gnps | GNPS spectrum similarity scores
gnps_chain_dp | Optimized GNPS Modified Cosine Similarity via Chain-DP
gnps_r | GNPS spectrum similarity scores
group | Grouping of numeric values by similarity
i2index | Input parameter check for subsetting operations
imputeMethods | Quantitative mass spectrometry data imputation
impute_bpca | Quantitative mass spectrometry data imputation
impute_fun | Quantitative mass spectrometry data imputation
impute_knn | Quantitative mass spectrometry data imputation
impute_matrix | Quantitative mass spectrometry data imputation
impute_min | Quantitative mass spectrometry data imputation
impute_MinDet | Quantitative mass spectrometry data imputation
impute_MinProb | Quantitative mass spectrometry data imputation
impute_mixed | Quantitative mass spectrometry data imputation
impute_mle | Quantitative mass spectrometry data imputation
impute_neighbour_average | Quantitative mass spectrometry data imputation
impute_QRILC | Quantitative mass spectrometry data imputation
impute_RF | Quantitative mass spectrometry data imputation
impute_with | Quantitative mass spectrometry data imputation
impute_zero | Quantitative mass spectrometry data imputation
isPeaksMatrix | Check functions
join | Relaxed Value Matching
join_gnps | GNPS spectrum similarity scores
join_gnps_r | GNPS spectrum similarity scores
localMaxima | Local Maxima
maxi | Maximum MS Intensity Value
medianPolish | Return the Median Polish (Robust Twoway Decomposition) of a matrix
navdist | Spectra Distance/Similarity Measurements
ndotproduct | Spectra Distance/Similarity Measurements
nentropy | Spectral entropy
neuclidean | Spectra Distance/Similarity Measurements
noise | Noise Estimation
normalizeMethods | Quantitative data normalisation
normalize_matrix | Quantitative data normalisation
nspectraangle | Spectra Distance/Similarity Measurements
ppm | PPM - Parts per Million
rbindFill | Combine R Objects by Row
reduce | Reduce overlapping numeric ranges to disjoined ranges
refineCentroids | Refine Peak Centroids
retry | Retry expression on failure
rla | Calculate relative log abundances
robustSummary | Return the Robust Expression Summary of a matrix
rowRla | Calculate relative log abundances
rt2character | Format Retention Time
rt2numeric | Format Retention Time
smooth | Smoothing
sumi | Summing MS Intensity Values
validPeaksMatrix | Validation functions
valleys | Find Peak Valleys
vapply1c | vapply wrappers
vapply1d | vapply wrappers
vapply1l | vapply wrappers
which.first | Which is the first/last TRUE value.
which.last | Which is the first/last TRUE value.