queryNeighbors: Query all neighbors

In BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

Description

Find all neighbors in one data set that are in range of each point in another query data set.

Usage

queryNeighbors(X, query, threshold, ..., BNINDEX, BNPARAM) 

Arguments

X	A numeric data matrix where rows are points and columns are dimensions.
query	A numeric query 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 ?"rangeQuery-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.

Details

The class of BNINDEX and BNPARAM will determine dispatch to specific methods. 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 ?"rangeQuery-methods" for more details.

Author(s)

Aaron Lun

See Also

rangeQueryKmknn and rangeQueryVptree for specific methods.

Examples

Y <- matrix(rnorm(100000), ncol=20)
Z <- matrix(rnorm(10000), ncol=20)
k.out <- queryNeighbors(Y, Z, threshold=3)
v.out <- queryNeighbors(Y, Z, threshold=3, BNPARAM=VptreeParam())

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

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

BiocNeighbors documentation built on Dec. 9, 2020, 2:01 a.m.