Package: multistateQTL 2.5.0

Amelia Dunstone

multistateQTL: Toolkit for the analysis of multi-state QTL data

A collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package 'multistateQTL' contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a 'QTLExperiment' object, which is based on the 'SummarisedExperiment' framework.

Authors:Christina Del Azodi [aut], Davis McCarthy [ctb], Amelia Dunstone [cre, aut]

multistateQTL_2.5.0.tar.gz
multistateQTL_2.5.0.zip(r-4.7)multistateQTL_2.5.0.zip(r-4.6)multistateQTL_2.5.0.zip(r-4.5)
multistateQTL_2.5.0.tgz(r-4.6-any)multistateQTL_2.5.0.tgz(r-4.5-any)
multistateQTL_2.5.0.tar.gz(r-4.7-any)multistateQTL_2.5.0.tar.gz(r-4.6-any)
multistateQTL_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
multistateQTL/json (API)

# Install 'multistateQTL' in R:

install.packages('multistateQTL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dunstone-a/multistateqtl/issues

On BioConductor:multistateQTL-2.5.0(bioc 3.24)multistateQTL-2.4.0(bioc 3.23)

functionalgenomics geneexpression sequencing visualization snp software

4.88 score 2 stars 15 scripts 19 exports 94 dependencies

Last updated from:1070219c1d. Checks:6 NOTE, 2 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	202
linux-devel-x86_64	ERROR	368
source / vignettes	OK	258
linux-release-x86_64	NOTE	353
macos-release-arm64	NOTE	176
macos-oldrel-arm64	NOTE	153
windows-devel	ERROR	250
windows-release	NOTE	256
windows-oldrel	NOTE	234
wasm-release	OK	167

Exports:callSignificance callSignificance<-getComplete getSignificant getTopHits plotCompareStates plotPairwiseSharing plotQTLClusters plotSimulationParams plotUpSet qtleEstimate qtleParams qtleParams2 qtleSimulate replaceNAs runPairwiseSharing runSignificantFeatures runTestMetrics simPerformance

Dependencies:abind ashr assertthat backports Biobase BiocGenerics bit bit64 checkmate circlize cli clue cluster codetools collapse colorspace ComplexHeatmap cpp11 crayon data.table DelayedArray digest doParallel dplyr etrunct farver fitdistrplus foreach generics GenomicRanges GetoptLong ggplot2 GlobalOptions glue gridExtra gtable hms invgamma IRanges irlba isoband iterators labeling lattice lifecycle magrittr mashr MASS Matrix MatrixGenerics matrixStats mixsqp mvtnorm pillar pkgconfig plyr png prettyunits progress purrr QTLExperiment R6 RColorBrewer Rcpp RcppArmadillo RcppGSL rjson rlang rmeta S4Arrays S4Vectors S7 scales Seqinfo shape softImpute SparseArray SQUAREM stringi stringr SummarizedExperiment survival tibble tidyr tidyselect truncnorm tzdb utf8 vctrs viridis viridisLite vroom withr XVector

multistateQTL: Orchestrating multi-state QTL analysis in R

Rendered frommultistateQTL.Rmdusingknitr::rmarkdown

Last update: 2025-03-17
Started: 2025-03-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Call associations as significant in each state.	callSignificance callSignificance,QTLExperiment-method callSignificance<-
Filter QTLExperiment based on missing data	getComplete
Filter to only QTLs significant in at least one state	getSignificant
Filter QTLExperiment to keep only top hits	getTopHits
Compare QTL between two states	plotCompareStates
Heatmap of pairwise QTL sharing with state-level annotations	plotPairwiseSharing
Heatmap of QTL across states	plotQTLClusters
Distribution of estimated simulation parameters	plotSimulationParams
Upset plot of QTL sharing between states with state-level annotations	plotUpSet
Estimate parameters from real data for simulating multi-state QTL summary statistics	qtleEstimate qtleParams2
Default qtle simulation parameters	qtleParams
Create simulated multistateQTL data for testing purposes	qtleSimulate
Return multistateQTL object with NAs filled in	replaceNAs
Compute the proportion of (significant) QTL shared by pairs of conditions	runPairwiseSharing
Function to summarize QTL summary statistics by feature ID	runSignificantFeatures
Classify multi-state QTL	runTestMetrics
Performance metrics for multistateQTL simulations	simPerformance