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Calculates permuted association plot coordinates

permutation_cutoff.Rd

Calculates matrix of apl coordinates when permuting the original data.

Usage

permutation_cutoff(
  caobj,
  mat,
  group = caobj@group,
  dims = caobj@dims,
  reps = 10,
  store_perm = FALSE,
  python = TRUE
)

Arguments

caobj

A "cacomp" object with principal row coordinates and standardized column coordinates calculated.

mat

A numeric matrix. For sequencing a count matrix, gene expression values with genes in rows and samples/cells in columns. Should contain row and column names.

group

Vector of indices of the columns to calculate centroid/x-axis direction.

dims

Integer. Number of CA dimensions to retain. Needs to be the same as in caobj!

reps

Integer. Number of permutations to perform.

store_perm

Logical. Whether permuted data should be stored in the CA object. This implementation dramatically speeds up computation compared to `svd()` in R.

python

DEPRACTED. A logical value indicating whether to use singular-value decomposition from the python package torch.

Value

List with permuted apl coordinates ("apl_perm") and, a list of saved ca components ("saved_ca") that allow for quick recomputation of the CA results. For random_direction_cutoff this saved_ca is empty.