network_reduction_by_p_value: Reduce the the entries in an adjacency matrix by thresholding...

In molnet-org/molnet: Predicting Differential Drug Response using Multi-Omics Networks

Description

(INTERNAL) This function reduces an adjacency matrix of correlations. If computations are done non-parallel corPvalueStudent is used. If computations are done in parallel, our own parallel implementation (corPvalueStudentParallel) of this function is used. function to calculate Student asymptotic p-values taking the number of samples into account. P-values are adjusted using p.adjust function. The upper triangle without diagonal entries of the adjacency matrix is passed for faster computation. P-values can be adjusted using one of several methods. A significance threshold 'alpha' can be set. All value entries below this threshold within the initial adjacency matrix will be set to NA. If a default cluster is registered with the 'parallel' package the computation will happen in parallel automatically.

Usage

network_reduction_by_p_value(
  adjacency_matrix,
  number_of_samples,
  reduction_alpha = 0.05,
  p_value_adjustment_method = "BH",
  parallel_chunk_size = 10^6
)

Arguments

adjacency_matrix	An adjacency matrix of correlation values.
number_of_samples	The number of samples used to calculate the correlation matrix.
reduction_alpha	A number indicating the alpha value applied for thresholding
p_value_adjustment_method	A string of the correction method applied to p-values. Passed to stats::p.adjust().
parallel_chunk_size	Number of p-values in smallest work unit when computing in parallel.

Value

A reduced adjacency matrix with NA's at martix entries with p-values below threshold.

Source

corPvalueStudent

Examples

adj_mat <- matrix(rnorm(36),nrow=6)
sum(is.na(adj_mat)) # before reduction
reduced_by_p_value_matrix <- network_reduction_by_p_value(adjacency_matrix=adj_mat,
                             number_of_samples=200, reduction_alpha = 0.05,
                             p_value_adjustment_method = "BH")
sum(is.na(reduced_by_p_value_matrix)) # after reduction

molnet-org/molnet documentation built on Dec. 21, 2021, 8:59 p.m.