get_diffnet_list_from_exp {snQTL} | R Documentation |
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 |
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
.