Package: imcExperiment 0.99.0

imcExperiment: Mass Cytometry S4 Class Structure Pipeline for Images

Containerizes cytometry data and allows for S4 class structure to extend slots related to cell morphology, spatial coordinates, phenotype network information, and unique cellular labeling.

Authors:Anthony Colombo [aut, cre]

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imcExperiment.pdf |imcExperiment.html✨
imcExperiment/json (API)

# Install 'imcExperiment' in R:
install.packages('imcExperiment', repos = c('https://arcolombo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/arcolombo/imcexperiment/issues

Datasets:

On CRAN:

softwareworkflowstepmultiplecomparisonimc

3.70 score 5 scripts 166 downloads 19 exports 36 dependencies

Last updated 3 years agofrom:02333b6844. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winERRORNov 05 2024
R-4.5-linuxERRORNov 05 2024
R-4.4-winERRORNov 05 2024
R-4.4-macERRORNov 05 2024
R-4.3-winERRORNov 05 2024
R-4.3-macERRORNov 05 2024

Exports:.checkSpatialDimensioncellIntensitycellIntensity<-getCoordinatesgetCoordinates<-getDistancegetDistance<-getLabelgetMorphologygetMorphology<-getNeighborhoodgetNeighborhood<-getNetworkgetNetwork<-imcExperimentimcExperimentToHyperFramepercentilenormalizeselectCasessubsetCase

Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraydeldirgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslpolyclipR6S4ArraysS4VectorsSingleCellExperimentSparseArrayspatstat.dataspatstat.geomspatstat.univarspatstat.utilsSummarizedExperimentsysUCSC.utilsXVectorzlibbioc

imcExperiment: containerization of IMC data

Anthony Colombo

Rendered fromexample.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2021-08-18
Started: 2020-03-03

Readme and manuals

Help Manual

Help pageTopics
the rows are the panel names, the columns are the single cells,the column are the single cells to match the SCE designs (scRNA).checkSpatialDimension
map to point pattern from imcExperiment class..imcExperimentToPPP
finds the intensities getter.cellIntensity cellIntensity,imcExperiment-method cellIntensity<- cellIntensity<-,imcExperiment,matrix-method
datadata
finds the spatial coords, getter.getCoordinates getCoordinates,imcExperiment-method getCoordinates<-,imcExperiment,matrix-method
Sets the coordinate positions of each cell (matrix), columns are X,Y positions.getCoordinates<-
re-assigns the distance matrix (rows are cells)getDistance<-
re-assigns morphological features can be stored (matrix) rows are cells and columns are Area, etc.getMorphology<-
finds the neighborhood information.getNeighborhood getNeighborhood,imcExperiment-method getNeighborhood<- getNeighborhood<-,imcExperiment,matrix-method
re-assigns the network assignment (matrix)getNetwork<-
imcdataimcdata
Initializes a imcExperiment and performs some rudimentary checks. Many of the arguments CAN be NULL; determination of which is required is done at run-time. A imcExperiment must contain at least the expressions and spatial/coordinate assays.imcExperiment
a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'.imcExperiment getDistance getDistance,imcExperiment-method getDistance<-,imcExperiment,matrix-method getLabel getLabel,imcExperiment-method getMorphology getMorphology,imcExperiment-method getMorphology<-,imcExperiment,matrix-method getNetwork getNetwork,imcExperiment-method getNetwork<-,imcExperiment,data.frame-method imcExperiment-class imcExperiment-method spatial
map to point pattern from imcExperiment class.imcExperimentToHyperFrame
given a matrix of intensity counts, perform min/max norm.percentilenormalize
subsets the imcExperiment to a case along with all slots for a selected multiple ROIs.selectCases selectCases,imcExperiment-method
subsets the imcExperiment to a case along with all slots for a single ROI, using for distance analysissubsetCase subsetCase,imcExperiment-method