Package: QTLExperiment 1.99.1

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]

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QTLExperiment.pdf |QTLExperiment.html✨
QTLExperiment/json (API)
NEWS

# 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-1.99.1(bioc 3.21)QTLExperiment-1.4.0(bioc 3.20)

functionalgenomicsdataimportdatarepresentationinfrastructuresequencingsnpsoftware

5.32 score 2 stars 1 packages 14 scripts 160 downloads 32 exports 66 dependencies

Last updated 5 days agofrom:c2a58bbc59. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
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Exports:.mashData_2_qtlebetasbetas<-cbindcoercecolData<-errorserrors<-feature_idfeature_id<-lfsrslfsrs<-mainExpNamemainExpName<-mash2qtlemockMASHRmockMASHR_FITmockQTLEmockSummaryStatsobjectVersionpvaluespvalues<-QTLExperimentrbindrowDatarowData<-state_idstate_id<-sumstats2qtleupdateObjectvariant_idvariant_id<-

Dependencies:abindashraskpassbackportsBiobaseBiocGenericsbitbit64checkmateclicollapsecpp11crayoncurlDelayedArraydplyretrunctfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrinvgammaIRangesirlbajsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimemixsqpopensslpillarpkgconfigprettyunitsprogresspurrrR6RcppRcppArmadillorlangS4ArraysS4VectorsSparseArraySQUAREMstringistringrSummarizedExperimentsystibbletidyrtidyselecttruncnormtzdbUCSC.utilsutf8vctrsvroomwithrXVector

An introduction to the QTLExperiment class

Christina B Azodi, Amelia Dunstone, Davis McCarthy

Rendered fromQTLExperiment.Rmdusingknitr::rmarkdownon Mar 20 2025.

Last update: 2025-03-07
Started: 2022-11-04

Readme and manuals

Help Manual

Help pageTopics
Mock data for the QTLExperiment objectmockMASHR mockMASHR_FIT mockQTLE mockSummaryStats
Named assay getters and settersbetas 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 QTLExperimentcolData colData,QTLExperiment-method colData<- colData<-,QTLExperiment,ANY-method colData<-,QTLExperiment,DataFrame-method colData<-,QTLExperiment,NULL-method qtle-colData
Combining QTLExperiment objectscbind,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 settersfeature_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 QTLExperimentqtle-rowData rowData rowData,QTLExperiment-method rowData<- rowData<-,QTLExperiment,DataFrame-method rowData<-,QTLExperiment,NULL-method rowData<-,QTLExperiment-method
Modify and view state IDqtle-state-id state_id state_id,QTLExperiment-method state_id<- state_id<-,QTLExperiment-method
Subsetting and replacing data in QTLExperiment objectsQTLe-subset subset,QTLExperiment-method [,QTLExperiment,ANY,ANY,ANY-method [,QTLExperiment,ANY,ANY-method [,QTLExperiment,ANY-method [<-,QTLExperiment,ANY,ANY,QTLExperiment-method
Return the version of a QTLExperiment objectobjectVersion objectVersion,QTLExperiment-method QTLe-version
An S4 class to represent QTL summary statistics.coerce,RangedSummarizedExperiment,QTLExperiment-method coerce,SummarizedExperiment,QTLExperiment-method QTLExperiment QTLExperiment-class
Coerce QTL summary statistics into a QTLExperiment objectsumstats2qtle
Update a QTLExperiment objectupdateObject updateObject,QTLExperiment-method