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)

## Arguments

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

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

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

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

## Value

A `Milo`

object with the `nhoodExpression`

slot populated.

## Details

This function computes the mean expression of each gene, subset by `subset.rows`

where present, across the cells contained within each neighbourhood.

## Examples

#> Constructing kNN graph with k:20

#> Checking valid object

#> Warning: Rownames not set on reducedDims - setting to row indices

#> [1] 1000 7