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runwSIR

Source: R/runwSIR.R
runwSIR.Rd

Perform wSIR on cells, based on the expression data and a reducedDim in a SingleCellExperiment or SpatialExperiment object

Usage

runwSIR(x, name = "wSIR", scores_only = FALSE, ...)

Arguments

x

A numeric matrix of normalised gene expression data where rows are features and columns are cells. Alternatively, a SingleCellExperiment or SpatialExperiment containing such a matrix

name

string to specify the name to store the result in the reducedDims of the output. Default is "wSIR"

scores_only

logical whether only the wSIR scores should be calculated. If FALSE additional information about the wSIR model will be stored in the attributes of the object. Default FALSE.

...

arguments passing to calculateWSIR

Value

If x is matrix-like, a list containing wSIR scores, loadings, etc. If x is a SingleCellExperiment or SpatialExperiment, the same object is returned with an additional slot in reducedDims(..., name) corresponding to the wSIR scores matrix. If scores_only = FALSE, then the attributes of the wSIR scores contain the following elements:

  • directions

  • estd

  • W

  • evalues

Examples

data(MouseData)
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’:
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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
#> Loading required package: GenomicRanges
#> Loading required package: stats4
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#> Attaching package: ‘generics’
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#>     setequal, union
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#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
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#>     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
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     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
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#>     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
library(SpatialExperiment)

sce <- SingleCellExperiment(assays = list(logcounts = t(sample1_exprs)),
reducedDims = list(spatial = sample1_coords))

sce <- runwSIR(x = sce, dim_red = "spatial")

spe <- SpatialExperiment(assays = list(logcounts = t(sample1_exprs)),
spatialCoords = as.matrix(sample1_coords))

spe <- runwSIR(x = spe, spatialCoords = TRUE)