This function calculates the mean expression of each feature in the Milo object stored in the assays slot. Neighbourhood expression data are stored in a new slot nhoodExpression.

calcNhoodExpression(x, assay = "logcounts", subset.row = NULL, exprs = NULL)



A Milo object with nhoods slot populated, alternatively a list containing a vector of cell indices; one per neighbourhood.


A character scalar that describes the assay slot to use for calculating neighbourhood expression.


A logical, integer or character vector indicating the rows of x to use for sumamrizing over cells in neighbourhoods.


If x is a list of neighbourhoods, exprs is a matrix of genes X cells to use for calculating neighbourhood expression.


A Milo object with the nhoodExpression slot populated.


This function computes the mean expression of each gene, subset by subset.rows where present, across the cells contained within each neighbourhood.


require(SingleCellExperiment) m <- matrix(rnorm(100000), ncol=100) milo <- Milo(SingleCellExperiment(assays=list(logcounts=m))) milo <- buildGraph(m, k=20, d=30)
#> Constructing kNN graph with k:20
milo <- makeNhoods(milo)
#> Checking valid object
#> Warning: Rownames not set on reducedDims - setting to row indices
milo <- calcNhoodExpression(milo) dim(nhoodExpression(milo))
#> [1] 1000 7