splitAltExps: Split off alternative features

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/splitAltExps.R


Split a SingleCellExperiment based on the feature type, creating alternative Experiments to hold features that are not in the majority set.


splitAltExps(x, f, ref = NULL)



A SingleCellExperiment object.


A character vector or factor of length equal to nrow(x), specifying the feature type of each row.


String indicating which level of f should be treated as the main set.


This function provides a convenient way to create a SingleCellExperiment with alternative Experiments. For example, a SingleCellExperiment with rows corresponding to all features can be quickly split into endogenous genes (main) and other alternative features like spike-in transcripts and antibody tags.

By default, the most frequent level of f is treated as the ref if the latter is not specified.


A SingleCellExperiment where each row corresponds to a feature in the main set. Each other feature type is stored as an alternative Experiment, accessible by altExp.


Aaron Lun

See Also

altExp, to access and manipulate the alternative Experiment fields.


example(SingleCellExperiment, echo=FALSE)
feat.type <- sample(c("endog", "ERCC", "CITE"), nrow(sce),
    replace=TRUE, p=c(0.8, 0.1, 0.1))

sce2 <- splitAltExps(sce, feat.type)

Example output

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package:MatrixGenericsThe following objects are masked frompackage: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
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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: S4Vectors

Attaching package:S4VectorsThe following object is masked frompackage:base:


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:BiobaseThe following object is masked frompackage:MatrixGenerics:


The following objects are masked frompackage:matrixStats:

    anyMissing, rowMedians

class: SingleCellExperiment 
dim: 164 100 
assays(2): counts logcounts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):
reducedDimNames(2): PCA tSNE
altExpNames(2): CITE ERCC

SingleCellExperiment documentation built on Nov. 8, 2020, 7:51 p.m.