nUniqueNeighDons: How many donors are contained among the nearest neighbors?

In Theorell/DepecheR: Determination of essential phenotypic elements of clusters in high-dimensional entities

How many donors are contained among the nearest neighbors?

Description

This function constructs a variable that for each event shows the number of donors in its nearest neighbor surroundings. It builds on the same idea as has been put forward in the Sconify package: -Burns TJ (2019). Sconify: A toolkit for performing KNN-based statistics for flow and mass cytometry data. R package version 1.4.0 and -Hart GT, Tran TM, Theorell J, Schlums H, Arora G, Rajagopalan S, et al. Adaptive NK cells in people exposed to Plasmodium falciparum correlate with protection from malaria. J Exp Med. 2019 Jun 3;216(6):1280–90. First, the k nearest neighbors are defined for cell x. Then, the number of donors in the k nearest neighbor cloud is returned.

Usage

nUniqueNeighDons(
  donorData,
  euclidSpaceData,
  neighRows = seq_len(nrow(as.matrix(donorData))),
  ctrlRows,
  kNeighK = max(100, round(nrow(as.matrix(euclidSpaceData))/10000)),
  kMeansK = max(1, round(nrow(as.matrix(euclidSpaceData))/1000))
)

Arguments

donorData	The donor information.
euclidSpaceData	The data cloud in which the nearest neighbors for the events should be identified. Can be a vector, matrix or dataframe.
neighRows	The rows in the dataset that correspond to the neighbors of the donorData points. This can be all the donorData points, or a subset, depending on the setup.
ctrlRows	Optionally, a set of control rows that are used to remove background signal from the neighRows data before sending the data back.
kNeighK	The number of nearest neighbors.
kMeansK	The number of clusters in the initial step of the algorithm. A higher number leads to shorter runtime, but potentially lower accuracy.

Value

An object of the same dimensions as donorData that has been smoothed.

Examples

data(testData)
data(testDataSNE)
euclidSpaceData <-
    testData[, c(
        "SYK", "CD16", "CD57", "EAT.2",
        "CD8", "NKG2C", "CD2", "CD56"
    )]
## Not run: 
nDonorsVector <- nUniqueNeighDons(
    donorData = as.numeric(testData$label),
    euclidSpaceData
)

## End(Not run)

Theorell/DepecheR documentation built on July 27, 2023, 8:13 p.m.