Core Utils for Mass Spectrometry Data

---

Documentation for package ‘MsCoreUtils’ version 1.14.1

• 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
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
distance	Spectra Distance/Similarity Measurements
dotproduct	Spectra Distance/Similarity Measurements
entropy	Spectral entropy
formatRt	Format Retention Time
getImputeMargin	Quantitative mass spectrometry data imputation
gnps	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
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
refineCentroids	Refine Peak Centroids
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.