graphSpatialFDR {miloR} | R Documentation

## Control the spatial FDR

### Description

Borrowing heavily from `cydar` which corrects for multiple-testing using a weighting scheme based on the volumetric overlap over hyperspheres. In the instance of graph neighbourhoods this weighting scheme can use graph connectivity or incorpate different within-neighbourhood distances for the weighted FDR calculation.

### Arguments

`x.nhoods` | A list of vertices and the constituent vertices of their neighbourhood
`graph` | The kNN graph used to define the neighbourhoods
`pvalues` | A vector of p-values calculated from a GLM or other appropriate statistical test for differential neighbourhood abundance
`k` | A numeric integer that determines the kth nearest neighbour distance to use for the weighted FDR. Only applicaple when using `weighting="k-distance"`.
`weighting` | A string scalar defining which weighting scheme to use. Choices are: max, k-distance, neighbour-distance.
`reduced.dimensions` | (optional) A `matrix` of cells X reduced dimensions used to calculate the kNN graph. Only necessary if this function is being used outside of `testNhoods` where the `Milo` object is not available
`distances` | (optional) A `matrix` of cell-to-cell distances or a list of distance matrices, 1 per neighbourhood. Only necessary if this function is being used outside of `testNhoods` where the `Milo` object is not available.
`indices` | (optional) A list of neighbourhood index vertices in the same order as the input neighbourhoods. Only used for the k-distance weighting.

### Details

Each neighbourhood is weighted according to the weighting scheme defined. k-distance uses the distance to the kth nearest neighbour of the index vertex, while neighbour-distance uses the average within-neighbourhood Euclidean distance in reduced dimensional space, and max uses the largest within-neighbourhood distance from the index vertex. The frequency-weighted version of the BH method is then applied to the p-values, as in `cydar`.

### Value

A vector of adjusted p-values

### Author(s)

Adapted by Mike Morgan, original function by Aaron Lun

### Examples

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[Package miloR version 1.2.0 Index]