Simulate Repeated Measures scRNA-seq Data using the RESCUE method
Arguments
- paramObj
RescueSimParams-class
object with no empty slots.
Value
SingleCellExperiment
object with
the data in the following slots
counts
Matrix of raw counts with genes represented by rows and cells represented by columns.
colData
- sampleID
Sample identifier
- subjectID
Subject identifier
- time
Timepoint identifier
- group
Group identifier
rowData
- deLog2FC
A
DataFrame
containing log2 fold change information for each gene. Each column corresponds to a non-reference experimental condition (e.g.,"time1"
,"group1"
,"time1_group1"
, etc.), and values represent gene-level log2 fold changes relative to the baseline condition ("time0"
,"group0"
, or"time0_group0"
depending on the design). The reference condition itself is not included as a column.
Examples
# Read in data
data("RecAM_sce")
# Calculate sim parameters for first 50 genes
RecAM_sce <- RecAM_sce[1:50,]
RecAM_params<-estRescueSimParams(RecAM_sce, sampleVariable = "sampleID",
subjectVariable = "subjectID", timepointVariable = "time")
# Simulate data
simDat=simRescueData(RecAM_params)
# Examine
library(SingleCellExperiment)
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
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#> Attaching package: ‘MatrixGenerics’
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#> 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
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#> as.data.frame, basename, cbind, colnames, dirname, do.call,
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#> 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’
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#> findMatches
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#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
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#> Vignettes contain introductory material; view with
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#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
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#> rowMedians
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#> anyMissing, rowMedians
counts(simDat)[1:5, 1:5]
#> cell_1 cell_2 cell_3 cell_4 cell_5
#> NOC2L 0 1 2 1 1
#> SCNN1D 0 0 0 0 0
#> AL391244.3 0 0 0 0 1
#> AL645728.1 0 0 0 1 0
#> AL691432.2 0 0 0 0 2