pool_across_neighbors {cellpypes} | R Documentation |
Sum up x across neighbors in a nearest neighbor graph.
Description
Neighbor pooling means that x is summed across the nearest neighbors.
Usage
pool_across_neighbors(x, neighbors)
Arguments
x |
Numeric vector. |
neighbors |
Nearest neighbor graph provided as NxK index matrix
(N observations, K neighbors) or NxN adjacency matrix.
Index matrices can be obtained with find_knn
(specifically the slot |
Value
Numeric vector of length x.
Examples
set.seed(42)
# simulate 30 cells without biological signal:
dummy_dat <- matrix(rpois(3000, .1), ncol=30)
# find 15 approximate nearest neighbors
neighbors <- find_knn(dummy_dat, k = 15)
# pool gene1 counts across neighbors:
neighbor_sum_gene1 <- pool_across_neighbors(dummy_dat[1,], neighbors$idx)
[Package cellpypes version 0.3.0 Index]