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MsCoreUtils

Core Utils for Mass Spectrometry Data

MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Functions (25)

aggregate_by_vector

Aggreagate quantitative features.

binning

Binning

check

Check functions

coerce

Coerce functions

colCounts

Counts the number of features

distance

Spectra Distance/Similarity Measurements

group

Grouping of numeric values by similarity

i2index

Input parameter check for subsetting operations

imputation

Quantitative mass spectrometry data imputation

localMaxima

Local Maxima

matching

Relaxed Value Matching

medianPolish

Return the Median Polish (Robust Twoway Decomposition) of a matrix

noise

Noise Estimation

normalize

Quantitative data normalisation

peakRegionMask

Peak Region Mask

ppm

PPM - Parts per Million

range

Range helper functions

rbindFill

Combine R Objects by Row

refineCentroids

Refine Peak Centroids

rla

Calculate relative log abundances rla calculates the relative log abundances (RLA, see reference) on a numeric vector. rowRla performs row-wise RLA calculations on a numeric matrix.

robustSummary

Return the Robust Expression Summary of a matrix

smooth

Smoothing

validation

Validation functions

valleys

Find Peak Valleys

vapply

vapply wrappers

MsCoreUtils

Core Utils for Mass Spectrometry Data

v1.2.0

Artistic-2.0

Authors

RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] (<https://orcid.org/0000-0002-1520-2268>), Johannes Rainer [aut] (<https://orcid.org/0000-0002-6977-7147>), Sebastian Gibb [aut] (<https://orcid.org/0000-0001-7406-4443>), Adriaan Sticker [ctb], Sigurdur Smarason [ctb], Thomas Naake [ctb]

Initial release

MsCoreUtils

Functions (25)

MsCoreUtils

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