calcNhoodExpression: Average expression within neighbourhoods

View source: R/calcNhoodExpression.R

calcNhoodExpressionR 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))


MikeDMorgan/miloR documentation built on Aug. 7, 2022, 8:21 a.m.