R/queryNeighbors-functions.R

In BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

##############
# Exhaustive #
##############

#' @export
#' @importFrom BiocParallel SerialParam 
rangeQueryExhaustive <- function(X, query, threshold, get.index=TRUE, get.distance=TRUE, BPPARAM=SerialParam(), precomputed=NULL, transposed=FALSE, subset=NULL, raw.index=FALSE, ...)
# Identifies nearest neighbours in 'X' from a query set.
#
# created 24 April 2020
{
    .template_range_query_exact(X, query, threshold, get.index=get.index, get.distance=get.distance, BPPARAM=BPPARAM, precomputed=precomputed, 
        transposed=transposed, subset=subset, raw.index=raw.index, 
        buildFUN=buildExhaustive, searchFUN=range_query_exhaustive, searchArgsFUN=.find_exhaustive_args, ...) 
}

#########
# KMKNN #
#########

#' @export
#' @importFrom BiocParallel SerialParam 
rangeQueryKmknn <- function(X, query, threshold, get.index=TRUE, get.distance=TRUE, BPPARAM=SerialParam(), precomputed=NULL, transposed=FALSE, subset=NULL, raw.index=FALSE, ...)
# Identifies nearest neighbours in 'X' from a query set.
#
# written by Aaron Lun
# created 19 June 2018
{
    .template_range_query_exact(X, query, threshold, get.index=get.index, get.distance=get.distance, BPPARAM=BPPARAM, precomputed=precomputed, 
        transposed=transposed, subset=subset, raw.index=raw.index, 
        buildFUN=buildKmknn, searchFUN=range_query_kmknn, searchArgsFUN=.find_kmknn_args, ...) 
}

###########
# VP-tree #
###########

#' @export
#' @importFrom BiocParallel SerialParam 
rangeQueryVptree <- function(X, query, threshold, get.index=TRUE, get.distance=TRUE, BPPARAM=SerialParam(), precomputed=NULL, transposed=FALSE, subset=NULL, raw.index=FALSE, ...)
# Identifies nearest neighbours in 'X' from a query set.
#
# written by Aaron Lun
# created 19 June 2018
{
    .template_range_query_exact(X, query, threshold, get.index=get.index, get.distance=get.distance, BPPARAM=BPPARAM, precomputed=precomputed, 
        transposed=transposed, subset=subset, raw.index=raw.index, 
        buildFUN=buildVptree, searchFUN=range_query_vptree, searchArgsFUN=.find_vptree_args, ...)
}