get_distance_matrix: Get the pair-wise distance matrix for an assay

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Get the pair-wise distance matrix for an assay

Usage

get_distance_matrix(
  scm,
  assay = "score",
  type = c("pearson", "spearman", "kendall", "euclidean", "manhattan", "canberra",
    "binary", "minkowski"),
  verbose = TRUE
)

Arguments

scm	scMethrix; Input scMethrix object
assay	string; The assay to use. Default is 'score'
type	string; The type of distance metric to use. Available options are "pearson", "spearman", "tau", "euclidean", "manhattan", "canberra", "binary", "minkowski". An aribitrary distance function can also be used, so long as the input takes just the specified matrix.
verbose	boolean; flag to output messages or not

Details

Utilizes mainly the bioDist package to determine various distance metrics to be used for later clustering.

Value

matrix; the distance matrix

See Also

https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/dist

https://www.bioconductor.org/packages//2.7/bioc/html/bioDist.html

Examples

data('scMethrix_data')
scMethrix_data <- impute_regions(scMethrix_data) 
get_distance_matrix(scMethrix_data,assay = "impute") 

# For an arbitrary distance function
library(bioDist)
fun <- bioDist::spearman.dist
get_distance_matrix(scMethrix_data,assay = "impute",type = bioDist::spearman.dist)

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.