Package: QTLExperiment 2.5.0

Amelia Dunstone

QTLExperiment: S4 classes for QTL summary statistics and metadata

QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the 'SummarizedExperiment' class and contains functions for creating, merging, and subsetting objects. 'QTLExperiment' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.

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

QTLExperiment_2.5.0.tar.gz
QTLExperiment_2.5.0.zip(r-4.7)QTLExperiment_2.5.0.zip(r-4.6)QTLExperiment_2.5.0.zip(r-4.5)
QTLExperiment_2.5.0.tgz(r-4.6-any)QTLExperiment_2.5.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
QTLExperiment/json (API)

# Install 'QTLExperiment' in R:

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

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

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

functionalgenomics dataimport datarepresentation infrastructure sequencing snp software

5.90 score 3 stars 1 packages 25 scripts 264 downloads 33 exports 56 dependencies

Last updated from:ceefea5332. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	189
linux-devel-x86_64	NOTE	303
source / vignettes	OK	251
linux-release-x86_64	NOTE	345
macos-release-arm64	NOTE	215
macos-oldrel-arm64	NOTE	186
windows-devel	NOTE	246
windows-release	NOTE	218
windows-oldrel	NOTE	202
wasm-release	OK	180

Exports:.mashData_2_qtle betas betas<-cbind coerce colData<-errors errors<-feature_id feature_id<-lfsrs lfsrs<-mainExpName mainExpName<-mash2qtle mockMASHR mockMASHR_FIT mockQTLE mockSummaryStats objectVersion pvalues pvalues<-QTLExperiment rbind rowData rowData<-state_id state_id<-subset sumstats2qtle updateObject variant_id variant_id<-

Dependencies:abind ashr backports Biobase BiocGenerics bit bit64 checkmate cli collapse cpp11 crayon DelayedArray dplyr etrunct generics GenomicRanges glue hms invgamma IRanges irlba lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mixsqp pillar pkgconfig prettyunits progress purrr R6 Rcpp RcppArmadillo rlang S4Arrays S4Vectors Seqinfo SparseArray SQUAREM stringi stringr SummarizedExperiment tibble tidyr tidyselect truncnorm tzdb utf8 vctrs vroom withr XVector

An introduction to the QTLExperiment class

Rendered fromQTLExperiment.Rmdusingknitr::rmarkdown

Last update: 2025-12-17
Started: 2022-11-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mock data for the QTLExperiment object	mockMASHR mockMASHR_FIT mockQTLE mockSummaryStats
Named assay getters and setters	betas betas,QTLExperiment-method betas<- betas<-,QTLExperiment-method errors errors,QTLExperiment-method errors<- errors<-,QTLExperiment-method lfsrs lfsrs,QTLExperiment-method lfsrs<- lfsrs<-,QTLExperiment-method pvalues pvalues,QTLExperiment-method pvalues<- pvalues<-,QTLExperiment-method qtle-assays
Coercing mash data objects into QTLe objects	.mashData_2_qtle .mashFit_2_qtle mash2qtle QTLe-coerce
Modify and view the colData of a QTLExperiment	colData colData,QTLExperiment-method colData<- colData<-,QTLExperiment,ANY-method colData<-,QTLExperiment,DataFrame-method colData<-,QTLExperiment,NULL-method qtle-colData
Combining QTLExperiment objects	cbind,QTLExperiment-method QTLe-combine rbind,QTLExperiment-method
Return the name of a QTLExperiment object.	mainExpName mainExpName,QTLExperiment-method mainExpName<- mainExpName<-,QTLExperiment,character_OR_NULL-method QTLe-name
Recover QTLExperiment IDs	.recover_qtle_ids QTLe-recover
Named rowData getters and setters	feature_id feature_id,QTLExperiment-method feature_id<- feature_id<-,QTLExperiment-method qtle-row_ids variant_id variant_id,QTLExperiment-method variant_id<- variant_id<-,QTLExperiment-method
rowData method for QTLExperiment	qtle-rowData rowData rowData,QTLExperiment-method rowData<- rowData<-,QTLExperiment,DataFrame-method rowData<-,QTLExperiment,NULL-method rowData<-,QTLExperiment-method
Modify and view state ID	qtle-state-id state_id state_id,QTLExperiment-method state_id<- state_id<-,QTLExperiment-method
Return the version of a QTLExperiment object	objectVersion objectVersion,QTLExperiment-method QTLe-version
An S4 class to represent QTL summary statistics.	coerce,RangedSummarizedExperiment,QTLExperiment-method coerce,SummarizedExperiment,QTLExperiment-method QTLExperiment QTLExperiment-class
Subsetting and replacing data in QTLExperiment objects	subset subset,QTLExperiment-method [,QTLExperiment,ANY,ANY,ANY-method [,QTLExperiment,ANY,ANY-method [,QTLExperiment,ANY-method [<-,QTLExperiment,ANY,ANY,QTLExperiment-method
Coerce QTL summary statistics into a QTLExperiment object	sumstats2qtle
Update a QTLExperiment object	updateObject updateObject,QTLExperiment-method