findNeighbors-methods: Find all neighbors in range

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

Description

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

Usage

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

Arguments

X

A numeric data matrix where rows are points and columns are dimensions. This can be missing if BNINDEX is supplied.

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 ?"findNeighbors-functions" for more details.

BNINDEX

A BiocNeighborIndex object containing precomputed index information. This can be missing if X and BNPARAM is supplied, see Details.

BNPARAM

A BiocNeighborParam object specifying the algorithm to use. This can be missing if BNINDEX is supplied, see Details.

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().

Value

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 ?"findNeighbors-functions" for more details.

Author(s)

Aaron Lun

See Also

rangeFindKmknn and rangeFindVptree for specific methods.

Examples

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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())

LTLA/BiocNeighbors documentation built on Sept. 18, 2021, 8:19 p.m.