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snQTL (version 0.2)

Spectral Network Quantitative Trait Loci (snQTL) Analysis

Description

A spectral framework to map quantitative trait loci (QTLs) affecting joint differential networks of gene co-Expression. Test the equivalence among multiple biological networks via spectral statistics. See reference Hu, J., Weber, J. N., Fuess, L. E., Steinel, N. C., Bolnick, D. I., & Wang, M. (2025) .

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Version

Install

install.packages('snQTL')

Version

0.2

License

GPL (>= 2)

Maintainer

Jiaxin Hu

Last Published

April 29th, 2025

Functions in snQTL (0.2)

snQTL_test_corrnet

Spectral network quantitative trait loci (snQTL) test
solvePMD

Solving symmetric Penalized Matrix Decomposition
kronecker_list

List Kronecker Product
rs_unfold-methods

Tensor Row Space Unfolding
ttm

Tensor Matrix Product (m-Mode Product)
unfold-methods

Tensor Unfolding
sLME

Calculate of sLME for matrices
ttl

Tensor Times List
symmPMD

Symmetric Penalized Matrix Decomposition.
diffnet_to_snQTL_stats

Test statistics for snQTL
get_diffnet_from_exp

The differential matrix
dim-methods

Mode Getter for Tensor
fold

General Folding of Matrix
as.tensor

Tensor Conversion
cs_unfold-methods

Tensor Column Space Unfolding
SSTD_R1

Sparse Symmetric Tensor Decomposition (SSTD)
Ops-methods

Conformable elementwise operators for Tensor
Tensor-class

S4 Class for a Tensor
BinarySearch

Search soft threshold
single_exp_to_snQTL_stats

Generate one single snQTL test statistics from expression data
l2n

L2 norm for vector
get_diffnet_list_from_exp

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

Soft threshold
rand_tensor

Tensor with Random Entries