findNeighbors: Find all neighbors in range
In BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

Description Usage Arguments Details Value Author(s) See Also Examples

Find all neighbors within a given distance for each point in a data set.

1	findNeighbors(X, threshold, ..., BNINDEX, BNPARAM)

`X`	A numeric data matrix where rows are points and columns are dimensions.
`threshold`	A numeric scalar or vector specifying the maximum distance for considering neighbors.
`...`	Further arguments to pass to specific methods. This is guaranteed to include `subset`, `get.index`, `get.distance` `BPPARAM` and `raw.index`. See `?"rangeFind-methods"` for more details.
`BNINDEX`	A BiocNeighborIndex object containing precomputed index information. This can be missing if `BNPARAM` is supplied, see Details.
`BNPARAM`	A BiocNeighborParam object specifying the algorithm to use. This can be missing if `BNINDEX` is supplied, see Details.

The class of BNINDEX and BNPARAM will determine the dispatch to specific functions. Only one of these arguments needs to be defined to resolve dispatch. However, if both are defined, they cannot specify different algorithms.

If BNINDEX is supplied, X does not need to be specified. In fact, any value of X will be ignored as all necessary information for the search is already present in BNINDEX. Similarly, any parameters in BNPARAM will be ignored.

If both BNINDEX and BNPARAM are missing, the function will default to the KMKNN algorithm by setting BNPARAM=KmknnParam().

A list is returned containing index, a list of integer vectors specifying the identities of the neighbors of each point; and distance, a list of numeric vectors containing the distances to those neighbors. See ?"rangeFind-methods" for more details.

Aaron Lun

rangeFindKmknn and rangeFindVptree for specific methods.

Y <- matrix(rnorm(100000), ncol=20)
k.out <- findNeighbors(Y, threshold=3)
a.out <- findNeighbors(Y, threshold=3, BNPARAM=VptreeParam())

k.dex <- buildKmknn(Y)
k.out2 <- findNeighbors(Y, threshold=3, BNINDEX=k.dex)
k.out3 <- findNeighbors(Y, threshold=3, BNINDEX=k.dex, BNPARAM=KmknnParam())

v.dex <- buildVptree(Y)
v.out2 <- findNeighbors(Y, threshold=3, BNINDEX=v.dex)
v.out3 <- findNeighbors(Y, threshold=3, BNINDEX=v.dex, BNPARAM=VptreeParam())