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-4.7-x86_64)bigQF_1.6.zip(r-4.7-arm64)bigQF_1.6.zip(r-4.6-x86_64)bigQF_1.6.zip(r-4.6-arm64)bigQF_1.6.zip(r-4.5-x86_64)
bigQF_1.6.tgz(r-4.6-x86_64)bigQF_1.6.tgz(r-4.6-arm64)bigQF_1.6.tgz(r-4.5-x86_64)bigQF_1.6.tgz(r-4.5-arm64)
bigQF_1.6.tar.gz(r-4.7-arm64)bigQF_1.6.tar.gz(r-4.7-x86_64)bigQF_1.6.tar.gz(r-4.6-arm64)bigQF_1.6.tar.gz(r-4.6-x86_64)
bigQF_1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bigQF/json (API)

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

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

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

On CRAN:

Conda:

4.33 score 6 stars 12 scripts 344 downloads 6 exports 8 dependencies

Last updated from:dbba639928. Checks:13 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING142
linux-devel-x86_64WARNING158
source / vignettesOK194
linux-release-arm64WARNING111
linux-release-x86_64WARNING127
macos-release-arm64WARNING125
macos-release-x86_64WARNING543
macos-oldrel-arm64WARNING192
macos-oldrel-x86_64WARNING381
windows-devel-arm64WARNING270
windows-devel-x86_64WARNING155
windows-release-arm64WARNING220
windows-release-x86_64WARNING131
windows-oldrel-x86_64WARNING143
wasm-releaseOK93

Exports:famSKATpQFseigenSKAT.matrixfreesparse.matrixfreessvd

Dependencies:bdsmatrixCompQuadFormcoxmelatticeMatrixnlmesurvivalsvd

SKAT, weights, and projections
Rendered fromskat-proj.Rmdusingknitr::rmarkdown

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

Matrix-free computations
Rendered frommatrix-free.Rmdusingknitr::rmarkdown

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

Checking pQF vs SKAT
Rendered fromcheck-vs-SKAT-2.Rmdusingknitr::rmarkdown

Last update: 2018-05-18
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