learn_covariance: Function to learn covariance structure across samples using...

Description Usage Arguments

View source: R/learn_covariance.R

Description

Function to learn covariance structure across samples using latent factors

Usage

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learn_covariance(
  input,
  anno,
  kinship_matrix = NULL,
  P = 20,
  same_ind_initial_weight = 0.01,
  kinship_matrix_initial_weight = 0.01,
  ...
)

Arguments

input

[genes x samples] Normalized (e.g. quantile normalized) matrix of log2 gene expression

anno

[samples x 2] data.frame with 'individual' and 'condition' columns. If a kinship matrix is provided the row and column names must correspond to the values used in the 'individual' column.

kinship_matrix

Representing relatedness between individuals. Optional.

P

Number of latent factors to model. suez can prune out unnecessary factors (in principle).

same_ind_initial_weight

Initialization.

kinship_matrix_initial_weight

Initialization.

...

passed to rstan::optimizing


davidaknowles/suez documentation built on March 20, 2021, 2:19 a.m.