calc_Minkowski_distances: calc_Minkowski_distances

In MarioniLab/geneBasisR: What the Package Does (One Line, Title Case)

calc_Minkowski_distances

Description

Function returns Minkowski distances for kNN-graphs constructed from counts matrix in sce (stored in assay logcounts) using specified genes.

Usage

calc_Minkowski_distances(
  sce,
  genes,
  batch = NULL,
  n.neigh = 5,
  nPC = NULL,
  genes.predict = rownames(sce),
  p.minkowski = 3,
  genes.discard = NULL,
  genes.discard_prefix = NULL,
  ...
)

Arguments

sce	SingleCellExperiment object containing gene counts matrix (stored in 'logcounts' assay).
genes	Character vector containing genes that are used to construct kNN-graph.
batch	Name of the field in colData(sce) to specify batch. Default batch=NULL if no batch is applied.
n.neigh	Positive integer > 1, specifying number of neighbors to use for kNN-graph. Default n.neigh=5.
nPC	Scalar (or NULL) specifying number of PCs to use for kNN-graph. Default nPC=NULL (no PCA).
genes.predict	Character vector containing genes for which we want to calculate Minkowsky distances. Default genes.predict = rownames(sce).
p.minkowski	Order of Minkowski distance. Default p.minkowski=3.
genes.discard	Character vector containing genes to be excluded from candidates (note that they still will be used for graphs construction. If you want to exclude them from graph construction as well, just discard them prior in sce object). Default = NULL and no genes will be discarded.
genes.discard_prefix	Character vector containing prefixes of genes to be excluded (e.g. Rpl for L ribosomal proteins. Note that they still will be used for graphs construction. If you want to exclude them from graph construction as well, just discard them prior in sce object). Default = NULL and no genes will be discarded.
...	Additional arguments

Value

data.frame, field 'gene' to gene from genes.predict; field 'dist' corresponds to calculated Minkowski distance.

Examples

require(SingleCellExperiment)
n_row = 1000
n_col = 100
sce = SingleCellExperiment(assays = list(logcounts = matrix(rnorm(n_row*n_col), ncol=n_col)))
rownames(sce) = as.character(1:n_row)
colnames(sce) = c(1:n_col)
sce$cell = colnames(sce)
genes = rownames(sce)
out = calc_Minkowski_distances(sce, genes)

MarioniLab/geneBasisR documentation built on June 30, 2023, 2:04 p.m.