Description Usage Arguments Details Value Examples
Get variable genes from normalized UMI counts using Fano Factor metric.
1 | RankGenes(object, ngenes_keep = 1000)
|
object |
A SingleCellExperiment object containing normalized expression values in |
ngenes_keep |
integer to return top ranking |
Compute Fano Factor metric for each gene. The metric computes the median absolute deviation of dispersion across multiple bins for each gene.
A SingleCellExperiment object with an additional column named HVG
in rowData
column.
The column stores a a logical value against each gene to indicate if it has been ranked within the top
ngenes_keep
. It also generates an additional column dispersion_norm
in rowData
to
store the dispersion metric against each gene.
1 2 3 4 5 6 7 8 9 | library(SingleCellExperiment)
ncells <- 100
ngenes <- 2000
x <- matrix(rpois(ncells*ngenes, lambda = 10), ncol=ncells, nrow=ngenes, byrow=TRUE)
rownames(x) <- paste0("Gene", seq_len(ngenes))
colnames(x) <- paste0("Cell", seq_len(ncells))
sce <- SingleCellExperiment(list(counts=x))
sce <- CountNormalize(sce)
sce <- RankGenes(sce)
|
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