internal_distance: Calculate the distance of all the points within a single...

In sbrn3/disscat: Calculates Distances Between Single Cell RNA Seq Categories

Description

Enables calculating internal mean, sd and se of the distance that points in a cluster to the centre of a cluster.

Usage

internal_distance(seurat_object, group = NULL, reduction = "pca",
  dims = 1:30, method, distance = "euclidean", output = "table")

Arguments

seurat_object	A seurat object
group	Seurat Categories or groups for which the distances between are calculated. Cell wise data.
reduction	Dimensionality reduction data to use
dims	Which dimensions to use
method	Cluster Distance methods to use. Options are "single", "complete", "average", "centroid", "ward", "mahalanobis". Further explanation for these methods is given in the details.
distance	Point to point distance to use. Options are "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"
output	Whether to output as a seurat object (with data stored within) or as a table containing the information.

Details

This is an internal helper method for the function InternalDistance.

Value

table of mean, sd and se of internal cluster distances

See Also

InternalDistance

Other internal_distance: InternalDistance, internal_linkage_distance, internal_mahalanobis_distance

sbrn3/disscat documentation built on Dec. 12, 2019, 7:54 a.m.