Muraro et al. (2016) Human Pancreas Single-Cell RNA-Seq Query Data
Source:R/data.R
QueryCellData.RdA SingleCellExperiment object containing human pancreas single-cell RNA-seq data from Muraro et al. (2016). This dataset serves as the query dataset in the scLearn package for cell type annotation.
Format
A SingleCellExperiment object with 19127 genes (rows) and 2122 cells (columns). The object contains:
- counts
Raw count matrix
- logcounts
Log-normalized expression values
- colData
Cell metadata including:
cell_type1: Cell type annotations
other metadata fields...
References
Muraro, M. J., Dharmadhikari, G., Grün, D., Groen, N., Dielen, T., Jansen, E., ... & van Oudenaarden, A. (2016). A single-cell transcriptome atlas of the human pancreas. Cell systems, 3(4), 385-394.
Examples
library(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: 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’:
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#>
#> findMatches
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, 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’:
#>
#> rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#>
#> anyMissing, rowMedians
data(QueryCellData)
# Access expression matrix
assay(QueryCellData, "logcounts")[1:5,1:5]
#> D31.6_62 D30.4_62 D28.4_85 D28.2_87 D30.5_79
#> A1BG-AS1__chr19 0 0 0.000000 0.000000 0
#> A1BG__chr19 0 0 0.000000 0.000000 0
#> A1CF__chr10 0 0 1.588734 2.822002 0
#> A2M-AS1__chr12 0 0 0.000000 0.000000 0
#> A2ML1__chr12 0 0 1.001412 0.000000 0
# Access cell metadata
head(colData(QueryCellData))
#> DataFrame with 6 rows and 3 columns
#> cell_type1 donor batch
#> <character> <character> <character>
#> D31.6_62 acinar D31 6
#> D30.4_62 acinar D30 4
#> D28.4_85 acinar D28 4
#> D28.2_87 acinar D28 2
#> D30.5_79 acinar D30 5
#> D28.2_42 acinar D28 2