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 |

`BNINDEX` |
A BiocNeighborIndex object containing precomputed index information.
This can be missing if |

`BNPARAM` |
A BiocNeighborParam object specifying the algorithm to use.
This can be missing if |

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.

1 2 3 4 5 6 7 8 9 10 11 | ```
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())
``` |

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

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