The VectraPolarisData
package provides two large multiplex
immunofluorescence datasets, collected using Vectra 3 and Vectra
Polaris
instruments. Data included a study of lung cancer and a study of ovarian
cancer, and are provided as objects of class SpatialExperiment
.
Now available in Bioconductor version 3.15! To install, use:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
}
BiocManager::install("VectraPolarisData")
Here you can load data from the package. Data from the lung cancer study are loaded below.
library(VectraPolarisData)
#> Loading required package: ExperimentHub
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#> union, unique, unsplit, which.max, which.min
#> Loading required package: AnnotationHub
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
#> Loading required package: SpatialExperiment
#> Loading required package: SingleCellExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: S4Vectors
#>
#> Attaching package: 'S4Vectors'
#> The following objects are masked from 'package:base':
#>
#> expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#>
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
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#> rowMedians
#> The following objects are masked from 'package:matrixStats':
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#> anyMissing, rowMedians
#> The following object is masked from 'package:ExperimentHub':
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#> cache
#> The following object is masked from 'package:AnnotationHub':
#>
#> cache
spe_lung <- HumanLungCancerV3()
#> see ?VectraPolarisData and browseVignettes('VectraPolarisData') for documentation
#> loading from cache
spe_lung
#> class: SpatialExperiment
#> dim: 8 1604786
#> metadata(1): clinical_data
#> assays(3): intensities nucleus_intensities membrane_intensities
#> rownames(8): cd19_opal_650 cd3_opal_520 ... dapi autofluorescence
#> rowData names(0):
#> colnames: NULL
#> colData names(124): cell_id tissue_category ... phenotype_cd4 sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : cell_x_position cell_y_position
#> imgData names(0):
Data from the ovarian cancer study are loaded below.
spe_ovarian <- HumanOvarianCancerVP()
#> see ?VectraPolarisData and browseVignettes('VectraPolarisData') for documentation
#> loading from cache
spe_ovarian
#> class: SpatialExperiment
#> dim: 10 1610431
#> metadata(1): clinical_data
#> assays(3): intensities nucleus_intensities membrane_intensities
#> rownames(10): ck_opal_780 ki67_opal_690 ... dapi autofluorescence
#> rowData names(0):
#> colnames: NULL
#> colData names(195): cell_id tissue_category ... phenotype_cd8 sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : cell_x_position cell_y_position
#> imgData names(0):
These datasets are provided as SpatialExperiment
class objects. More
detailed information about these datasets is available in the package
vignette.