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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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
imcExperiment/json (API)

# Install 'imcExperiment' in R:

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

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

Datasets:

data - Data
imcdata - Imcdata

On CRAN:

software workflowstep multiplecomparison imc

3.70 score 6 scripts 281 downloads 19 exports 24 dependencies

Last updated from:02333b6844. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	246
source / vignettes	OK	272
linux-release-x86_64	ERROR	260
macos-release-arm64	ERROR	166
macos-oldrel-arm64	ERROR	178
windows-devel	ERROR	170
windows-release	ERROR	191
windows-oldrel	ERROR	190
wasm-release	OK	112

Exports:.checkSpatialDimension cellIntensity cellIntensity<-getCoordinates getCoordinates<-getDistance getDistance<-getLabel getMorphology getMorphology<-getNeighborhood getNeighborhood<-getNetwork getNetwork<-imcExperiment imcExperimentToHyperFrame percentilenormalize selectCases subsetCase

Dependencies:abind Biobase BiocGenerics DelayedArray deldir generics GenomicRanges IRanges lattice Matrix MatrixGenerics matrixStats polyclip S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray spatstat.data spatstat.geom spatstat.univar spatstat.utils SummarizedExperiment XVector

imcExperiment: containerization of IMC data

Rendered fromexample.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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
data	data
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<-
imcdata	imcdata
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 analysis	subsetCase subsetCase,imcExperiment-method