A small SummarizedExperiment with 10000 genes and 8 samples. Includes a treatment effect in the first 500 genes.
Format
A SummarizedExperiment with:
- assays
counts - raw count matrix
- colData
sample_id, treatment (control/treated), batch (A/B)
- rowData
gene_id, gene_symbol
Examples
library(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
#> Loading required package: generics
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#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
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#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#> setequal, union
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#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
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#> IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
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#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#> mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#> unsplit, which.max, which.min
#> Loading required package: S4Vectors
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#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
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#> findMatches
#> The following objects are masked from ‘package:base’:
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#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: Seqinfo
#> 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
data(example_se)
example_se
#> class: SummarizedExperiment
#> dim: 10000 8
#> metadata(0):
#> assays(1): counts
#> rownames(10000): gene1 gene2 ... gene9999 gene10000
#> rowData names(2): gene_id gene_symbol
#> colnames(8): sample1 sample2 ... sample7 sample8
#> colData names(3): sample_id treatment batch
colData(example_se)
#> DataFrame with 8 rows and 3 columns
#> sample_id treatment batch
#> <character> <character> <character>
#> sample1 sample1 control A
#> sample2 sample2 control B
#> sample3 sample3 control A
#> sample4 sample4 control B
#> sample5 sample5 treated A
#> sample6 sample6 treated B
#> sample7 sample7 treated A
#> sample8 sample8 treated B