Cardinal: A mass spectrometry imaging toolbox for statistical analysis
Version 1.8.0

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

AuthorKylie A. Bemis <k.bemis@northeastern.edu>
Bioconductor views Classification Clustering ImagingMassSpectrometry Infrastructure Lipidomics MassSpectrometry Normalization Proteomics Software
Date of publicationNone
MaintainerKylie A. Bemis <k.bemis@northeastern.edu>
LicenseArtistic-2.0
Version1.8.0
URL http://www.cardinalmsi.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Cardinal")

Getting started

Package overview
README.md

Popular man pages

Cardinal-package: Mass spectrometry imaging tools
generateSpectrum: Generate a Simulated Spectrum
MSImageProcess-class: Class Containing Mass Spectral Pre-Processing Information
pixelApply-methods: Apply Functions over Imaging Datasets
PLS-methods: Partial Least Squares
smoothSignal-methods.R: Smooth the Feature-Vectors of an Imaging Dataset
spatialKMeans-methods: Spatially-Aware K-Means Clustering
See all...

All man pages Function index File listing

Man pages

batchProcess-methods: Batch Pre-Processing on an Imaging Dataset
Binmat-class: On-Disk Matrix Class Using On-Demand Disk Reads
Cardinal-package: Mass spectrometry imaging tools
colors-functions: Color Palettes for Imaging
coord-methods: Retrieve Pixel Coordinates from iSets
coregister-methods: Coregister Images
cvApply-methods: Apply Cross-Validated Analysis to Imaging Datasets
generateImage: Generate a Simulated Image
generateSpectrum: Generate a Simulated Spectrum
Hashmat-class: Sparse Matrix Class Using Lists as Hash Tables
IAnnotatedDataFrame-class: Class Containing Measured Variables and Their Meta-Data...
ImageData-class: Class Containing Arrays of Imaging Data
imageData-methods: Retrieve Image Data from iSets
image-methods: Plot the Pixel-Space of an Imaging Dataset
iSet-class: Class to Contain High-Throughput Imaging Experiment Data and...
MIAPE-Imaging-class: Class for Storing Mass Spectrometry Imaging Experiment...
MSImageData-class: Class Containing Mass Spectrometry Image Data
MSImageProcess-class: Class Containing Mass Spectral Pre-Processing Information
MSImageSet-class: Class to Contain Mass Spectrometry Imaging Experiment Data
mz-methods: Retrieve m/z-values from MSImageSets
normalize-methods: Normalize an Imaging Dataset
OPLS-methods: Orthogonal Partial Least Squares
PCA-methods: Principal Components Analysis
peakAlign-methods: Peak Align an Imaging Dataset
peakFilter-methods: Peak Filter an Imaging Dataset
peakPick-methods: Peak Pick an Imaging Dataset
pixelApply-methods: Apply Functions over Imaging Datasets
pixelData-methods: Retrieve Information on Pixels in iSet-derived Classes
pixelNames-methods: Retrieve Pixel Names from iSets
pixels-methods: Retrieve Pixel or Feature Indices Based on Metadata
plot-methods: Plot the Feature-Space of an Imaging Dataset
PLS-methods: Partial Least Squares
processingData-methods: Retrieve Pre-Processing Information from MSImageSets
readMSIData: Read Mass Spectrometry Imaging Data Files
reduceBaseline-methods: Reduce the Baseline for an Imaging Dataset
reduceDimension-methods: Reduce the Dimension of an Imaging Dataset
ResultSet-class: Class to Contain Analysis Results for Imaging Experiments
select-methods: Select Regions of an Imaging Dataset
SImageData-class: Class Containing Sparse Image Data
SImageSet-class: Class to Contain Pixel-Sparse Imaging Data
smoothSignal-methods.R: Smooth the Feature-Vectors of an Imaging Dataset
spatialKMeans-methods: Spatially-Aware K-Means Clustering
spatialShrunkenCentroids-methods: Spatially-Aware Shrunken Centroid Clustering and...
standardizeSamples-methods: Standardize the Samples in an Imaging Dataset
topLabels-methods: Retrieve Top-Ranked Labels from Analysis Results

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/DataClasses.R
R/analysis-OPLS.R
R/analysis-PCA.R
R/analysis-PLS.R
R/analysis-spatialKMeans.R
R/analysis-spatialShrunkenCentroids.R
R/colors.R
R/combine.R
R/contrast.R
R/coregister.R
R/fastmap.R
R/format.R
R/generateImage.R
R/generateSpectrum.R
R/image3d.R
R/interpolate.R
R/log.R
R/math.R
R/methods-Binmat.R
R/methods-Hashmat.R
R/methods-IAnnotatedDataFrame.R
R/methods-ImageData.R
R/methods-MIAPE-Imaging.R
R/methods-MSImageData.R
R/methods-MSImageProcess.R
R/methods-MSImageSet.R
R/methods-ResultSet.R
R/methods-SImageData.R
R/methods-SImageSet.R
R/methods-iSet.R
R/nipals.R
R/normalize.R
R/plotting-MSImageSet.R
R/plotting-ResultSet.R
R/plotting-SImageSet.R
R/processing-batchProcess.R
R/processing-normalize.R
R/processing-peakAlign.R
R/processing-peakFilter.R
R/processing-peakPick.R
R/processing-reduceBaseline.R
R/processing-reduceDimension.R
R/processing-smoothSignal.R
R/processing-standardizeSamples.R
R/readAnalyze.R
R/readImzML.R
R/readMSIData.R
R/smooth.R
R/spatial.R
R/summary.R
R/topLabels.R
R/utils.R
R/zzz.R
README.md
TODO
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/Cardinal-development.R
inst/doc/Cardinal-development.Rnw
inst/doc/Cardinal-development.pdf
inst/doc/Cardinal-walkthrough.R
inst/doc/Cardinal-walkthrough.Rnw
inst/doc/Cardinal-walkthrough.pdf
inst/tests
man
man/Binmat-class.Rd
man/Cardinal-package.Rd
man/Hashmat-class.Rd
man/IAnnotatedDataFrame-class.Rd
man/ImageData-class.Rd
man/MIAPE-Imaging-class.Rd
man/MSImageData-class.Rd
man/MSImageProcess-class.Rd
man/MSImageSet-class.Rd
man/OPLS-methods.Rd
man/PCA-methods.Rd
man/PLS-methods.Rd
man/ResultSet-class.Rd
man/SImageData-class.Rd
man/SImageSet-class.Rd
man/batchProcess-methods.Rd
man/colors-functions.Rd
man/coord-methods.Rd
man/coregister-methods.Rd
man/cvApply-methods.Rd
man/generateImage.Rd
man/generateSpectrum.Rd
man/iSet-class.Rd
man/image-methods.Rd
man/imageData-methods.Rd
man/mz-methods.Rd
man/normalize-methods.Rd
man/peakAlign-methods.Rd
man/peakFilter-methods.Rd
man/peakPick-methods.Rd
man/pixelApply-methods.Rd
man/pixelData-methods.Rd
man/pixelNames-methods.Rd
man/pixels-methods.Rd
man/plot-methods.Rd
man/processingData-methods.Rd
man/readMSIData.Rd
man/reduceBaseline-methods.Rd
man/reduceDimension-methods.Rd
man/select-methods.Rd
man/smoothSignal-methods.R.rd
man/spatialKMeans-methods.Rd
man/spatialShrunkenCentroids-methods.Rd
man/standardizeSamples-methods.Rd
man/topLabels-methods.Rd
src
src/OBO-IMS.h
src/OBO-MS.h
src/OBO-UO.h
src/dynamicAlign.c
src/fastmap.c
src/fastmap.h
src/localMaxima.c
src/pugiconfig.h
src/pugixml.cpp
src/pugixml.h
src/readAnalyze.cpp
src/readImzML.cpp
src/smooth.c
src/spatial.c
src/utils.cpp
src/utils.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test-Hashmat.R
tests/testthat/test-IAnnotatedDataFrame.R
tests/testthat/test-ImageData.R
tests/testthat/test-MIAPE-Imaging.R
tests/testthat/test-MSImageData.R
tests/testthat/test-MSImageProcess.R
tests/testthat/test-MSImageSet.R
tests/testthat/test-OPLS.R
tests/testthat/test-PCA.R
tests/testthat/test-PLS.R
tests/testthat/test-SImageData.R
tests/testthat/test-SImageSet.R
tests/testthat/test-fastmap.R
tests/testthat/test-generatePositionArray.R
tests/testthat/test-iSet.R
tests/testthat/test-nipals.R
tests/testthat/test-processing.R
tests/testthat/test-spatialKMeans.R
tests/testthat/test-spatialShrunkenCentroids.R
vignettes
vignettes/Cardinal-development.Rnw
vignettes/Cardinal-walkthrough.Rnw
vignettes/Cardinal.bib
vignettes/pig206-mz256.pdf
vignettes/pig206-optical.png
vignettes/pig206-sscg.pdf
vignettes/preprocessingRoughDraft.pdf
vignettes/rcc-MH0204_33.png
vignettes/rcc-mz810.pdf
vignettes/rcc-sscg.pdf
Cardinal documentation built on May 20, 2017, 10 p.m.

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All documentation is copyright its authors; we didn't write any of that.