Package: snQTL 0.2

Jiaxin Hu

snQTL: Spectral Network Quantitative Trait Loci (snQTL) Analysis

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) <doi:10.1371/journal.pcbi.1012953>.

Authors:Jiaxin Hu [aut, cre, cph], Miaoyan Wang [aut, cph]

snQTL_0.2.tar.gz
snQTL_0.2.zip(r-4.7-any)snQTL_0.2.zip(r-4.6-any)
snQTL_0.2.tar.gz(r-4.7-any)snQTL_0.2.tar.gz(r-4.6-any)
snQTL_0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
snQTL/json (API)

# Install 'snQTL' in R:
install.packages('snQTL', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 162 downloads 17 exports 7 dependencies

Last updated from:c24880288e. Checks:4 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE115
source / vignettesOK171
linux-releaseNOTE118
windows-develNOTE64
windows-releaseNOTE71
wasm-releaseOK98

Exports:as.tensorcs_unfolddiffnet_to_snQTL_statsfoldget_diffnet_from_expget_diffnet_list_from_expkronecker_listrand_tensorrs_unfoldsingle_exp_to_snQTL_statssLMEsnQTL_test_corrnetSSTD_R1symmPMDttlttmunfold

Dependencies:latticeMASSMatrixrARPACKRcppRcppEigenRSpectra

Readme and manuals

Help Manual

Help pageTopics
Tensor Conversionas.tensor
Search soft thresholdBinarySearch
Tensor Column Space Unfoldingcs_unfold cs_unfold,Tensor-method cs_unfold-methods
Test statistics for snQTLdiffnet_to_snQTL_stats
Mode Getter for Tensordim,Tensor-method dim-methods
General Folding of Matrixfold
The differential matrixget_diffnet_from_exp
Get the list of differential matrix from a list of expression dataget_diffnet_list_from_exp
List Kronecker Productkronecker_list
L2 norm for vectorl2n
Conformable elementwise operators for TensorOps,array,Tensor-method Ops,numeric,Tensor-method Ops,Tensor,array-method Ops,Tensor,numeric-method Ops,Tensor,Tensor-method Ops-methods
Tensor with Random Entriesrand_tensor
Tensor Row Space Unfoldingrs_unfold rs_unfold,Tensor-method rs_unfold-methods
Generate one single snQTL test statistics from expression datasingle_exp_to_snQTL_stats
Calculate of sLME for matricessLME
Spectral network quantitative trait loci (snQTL) testsnQTL_test_corrnet
Soft thresholdsoft
Solving symmetric Penalized Matrix DecompositionsolvePMD
Sparse Symmetric Tensor Decomposition (SSTD)SSTD_R1
Symmetric Penalized Matrix Decomposition.symmPMD
S4 Class for a TensorTensor Tensor-class
Tensor Times Listttl
Tensor Matrix Product (m-Mode Product)ttm
Tensor Unfoldingunfold unfold,Tensor-method unfold-methods