romic (version 1.3.3)

calculate_sample_mahalanobis_distances: Calculate Sample Mahalanobis Distances

Description

Determine each samples distance from the center of the data using Mahalanobis distance.

Usage

calculate_sample_mahalanobis_distances(
  tomic,
  value_var = NULL,
  max_pcs = 10,
  scale = FALSE
)

Value

The samples tibble with a new column `pc_distance` which contains the Mahalanobis distances of individual samples from the PC elipsoid

Arguments

tomic

Either a tidy_omic or triple_omic object

value_var

the measurement variable to use for calculating distances

max_pcs

the maximum number of principal components to used for representing the covariance matrix.

scale

if TRUE then the data will be scaled before calculating distances

Details

Since `romic` is built around using tall data where there are more features than samples calculating Mahalanobis distance off of the covariance matrix is not possible. Instead, we use SVD to create a low-dimensional representation of the covariance matrix and calculate distances from the center of the data in this space. This essentially involves weighting the principal components by their loadings.

Examples

calculate_sample_mahalanobis_distances(brauer_2008_tidy)