get_similarity_matrix: Generate a similarity matrix

In MultIS: Reconstruction of Clones from Integration Site Readouts and Visualization

Description

Generate a similarity matrix

Usage

get_similarity_matrix(
  readouts,
  self = NULL,
  upper = TRUE,
  method = "rsquared",
  strategy = "atLeastOne",
  min_measures = 3L,
  post_norm = TRUE,
  parallel = FALSE
)

Arguments

readouts	The readouts that are used to generate the similarity matrix
self	Values to set on the diagonal of the matrix. If NULL, the values that are returned by the method are used.
upper	Only used with "rsquared". If TRUE, generates the upper triangle.
method	The method to use as a string. Possible values for the string are "rsquared" and any method that is accepted by stats::dist. In case of stats::dist we are using the change in the values over time / compartments (columns).
strategy	Defines the strategy how to treat 0 / NA values. Considering a pair (two lines), **atLeastOne** ignores all columns, where both are 0. **all** takes all measures into account, independent whether they are 0 or not.
min_measures	Minimum number of measures to compare two integration sites (rows). If there are less measures, the similarity entry is NA.
post_norm	Normalize the similarity matrix to [0,1] scale.
parallel	Whether parallelism should be used. Number of cores is set by option mc.cores. If unset, parallel::detectCores is used.

Value

A similarity matrix.

MultIS documentation built on Aug. 6, 2021, 5:07 p.m.