scHOT_buildFromSCE

Create scHOT object from a SingleCellExperiment object

scHOT_buildFromSCE(
  sce,
  assayName = "counts",
  positionType = NULL,
  positionColData = NULL
)

Arguments

sce	A SingleCellExperiment object
assayName	is a single assay to pull out from sce as the expression matrix input of scHOT
positionType	A string indicates the position type, either trajectory or spatial
positionColData	Strings indicate the position information stored in colData. If positionType is "trajectory" then positionColData should be a sortable vector if positionType is "spatial" then positionColData should be a matrix type object.

Value

A scHOT object

Examples

library(SingleCellExperiment)
#> Loading required package: SummarizedExperiment
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:parallel’:
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package: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, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:base’:
#> 
#>     expand.grid
#> 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")'.
#> Loading required package: DelayedArray
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘matrixStats’
#> The following objects are masked from ‘package:Biobase’:
#> 
#>     anyMissing, rowMedians
#> 
#> Attaching package: ‘DelayedArray’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
#> The following objects are masked from ‘package:base’:
#> 
#>     aperm, apply, rowsum
dat <- rbind(rnorm(50), rnorm(50), rnorm(50))
colnames(dat) <- paste0("cell_", 1:ncol(dat))
rownames(dat) <- c("gene_1","gene_2", "gene_2")

sce <- SingleCellExperiment::SingleCellExperiment(assays =
S4Vectors::SimpleList(counts = dat))
scHOT <- scHOT_buildFromSCE(sce)