get_similarity_matrix {MultIS}

Generate a similarity matrix

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.