get_diffnet_list_from_exp: Get the list of differential matrix from a list of expression...

In snQTL: Spectral Network Quantitative Trait Loci (snQTL) Analysis

Get the list of differential matrix from a list of expression data

Description

Given a list of expression data, X_1, ..., X_K, compute the list of differential matrix

D^{(k,l)} = N(X_l) - N(X_k), k < l,

where N() is the covariance matrix, or the weighted adjacency matrices defined as

N_{ij} = |corr(i, j)|^beta

for some constant beta > 0, 1 <= i, j <= p. Let N represent the regular correlation matrix when beta=0, and covariance matrix when beta<0. In total, we will have K*(K-1)/2 pairwise differential networks in the list.

If trans = TRUE, we let N_{ij} = 0 if i, j are from the same region based on location. Under gene co-expression context, trans-correlation usually refer to the correlation between two genes i, j from two chromosomes.

Usage

get_diffnet_list_from_exp(
  exp_list,
  adj.beta = -1,
  trans = FALSE,
  location = NULL
)

Arguments

exp_list	a list of nk-by-p matrices from the K populations. Rows are samples/observations, while columns are the features.
adj.beta	Power to transform correlation matrices to weighted adjacency matrices by N_{ij} = |r_ij|^adj.beta where r_ij represents the Pearson's correlation. When adj.beta=0, the correlation marix is used. When adj.beta<0, the covariance matrix is used. The default value is adj.beta=-1.
trans	logic variable, whether to only consider the trans-correlation (between genes from two different chromosomes or regions)
location	vector, the (chromosome) locations for items

Value

A list of p-by-p differential matrix D^{(k,l)}, k < l.

snQTL documentation built on June 8, 2025, 1:53 p.m.