Package: bigQF 1.6

bigQF: Quadratic Forms in Large Matrices

A computationally-efficient leading-eigenvalue approximation to tail probabilities and quantiles of large quadratic forms, in particular for the Sequence Kernel Association Test (SKAT) used in genomics <doi:10.1002/gepi.22136>. Also provides stochastic singular value decomposition for dense or sparse matrices.

Authors:Thomas Lumley

bigQF_1.6.tar.gz
bigQF_1.6.zip(r-4.5)bigQF_1.6.zip(r-4.4)bigQF_1.6.zip(r-4.3)
bigQF_1.6.tgz(r-4.4-x86_64)bigQF_1.6.tgz(r-4.4-arm64)bigQF_1.6.tgz(r-4.3-x86_64)bigQF_1.6.tgz(r-4.3-arm64)
bigQF_1.6.tar.gz(r-4.5-noble)bigQF_1.6.tar.gz(r-4.4-noble)
bigQF_1.6.tgz(r-4.4-emscripten)bigQF_1.6.tgz(r-4.3-emscripten)
bigQF.pdf |bigQF.html✨
bigQF/json (API)

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

Peer review:

Bug tracker:https://github.com/tslumley/bigqf/issues

Datasets:
  • SKAT.example - Data example from SKAT package
  • Z1 - Example data, from seqMeta package
  • Z2 - Example data, from seqMeta package
  • kins - Example data, from seqMeta package
  • pheno1 - Example data, from seqMeta package
  • pheno2 - Example data, from seqMeta package
  • sequence - Simulated human DNA variant sequence

On CRAN:

4.30 score 6 stars 11 scripts 211 downloads 6 exports 8 dependencies

Last updated 3 years agofrom:dbba639928. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-win-x86_64WARNINGNov 06 2024
R-4.5-linux-x86_64WARNINGNov 06 2024
R-4.4-win-x86_64WARNINGNov 06 2024
R-4.4-mac-x86_64WARNINGNov 06 2024
R-4.4-mac-aarch64WARNINGNov 06 2024
R-4.3-win-x86_64WARNINGNov 06 2024
R-4.3-mac-x86_64WARNINGNov 06 2024
R-4.3-mac-aarch64WARNINGNov 06 2024

Exports:famSKATpQFseigenSKAT.matrixfreesparse.matrixfreessvd

Dependencies:bdsmatrixCompQuadFormcoxmelatticeMatrixnlmesurvivalsvd

Checking pQF vs SKAT

Thomas Lumley

Rendered fromcheck-vs-SKAT-2.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2018-05-18
Started: 2018-05-18

Matrix-free computations

Thomas Lumley

Rendered frommatrix-free.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2021-10-27
Started: 2021-10-27

SKAT, weights, and projections

Thomas Lumley

Rendered fromskat-proj.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2021-10-30
Started: 2018-05-18

Readme and manuals

Help Manual

Help pageTopics
Quadratic Forms in Large MatricesbigQF-package bigQF
Implicit matrix for family-based SKAT testfamSKAT famSKAT.GENESIS.nullMixedModel famSKAT.lmekin update.famSKAT_genesis update.famSKAT_lmekin
Tail probabilities for quadratic formspQF
Stochastic singular value decompositionseigen ssvd
Example data, from seqMeta packagekins pheno1 pheno2 seqMetaExample Z1 Z2
Simulated human DNA variant sequencesequence
Data example from SKAT packageSKAT.example
Make 'matrix-free' object for SKAT testSKAT.matrixfree SKAT.matrixfree.glm SKAT.matrixfree.lm SKAT.matrixfree.lmekin
Make 'matrix-free' object from (sparse) Matrixsparse.matrixfree