calcNhoodExpression {miloR} | R Documentation

## Average expression within neighbourhoods

### Description

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`.

### Usage

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

### Arguments

`x` | A `Milo` object with `nhoods` slot populated, alternatively a NxM indicator matrix of N cells and M nhoods.
`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.

### Details

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

### Value

A `Milo` object with the `nhoodExpression` slot populated.

### Author(s)

Mike Morgan

### Examples

    require(SingleCellExperiment)
    m <- matrix(rnorm(100000), ncol=100)
    milo <- Milo(SingleCellExperiment(assays=list(logcounts=m)))
    milo <- buildGraph(m, k=20, d=30)
    milo <- makeNhoods(milo)
    milo <- calcNhoodExpression(milo)
    dim(nhoodExpression(milo))

[Package miloR version 1.2.0 Index]