Package: QTLExperiment 1.5.0

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, ctb]

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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-1.5.0(bioc 3.21)QTLExperiment-1.4.0(bioc 3.20)

functionalgenomics dataimport datarepresentation infrastructure sequencing snp software

4.77 score 1 stars 1 packages 13 scripts 116 downloads 39 exports 67 dependencies

Last updated 2 months agofrom:658a8b5acb. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	NOTE	Dec 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	NOTE	Dec 19 2024
R-4.4-mac	NOTE	Dec 19 2024
R-4.3-win	NOTE	Dec 19 2024
R-4.3-mac	NOTE	Dec 19 2024

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

Dependencies:abind ashr askpass backports Biobase BiocGenerics bit bit64 checkmate cli collapse cpp11 crayon curl DelayedArray dplyr etrunct fansi generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue hms httr invgamma IRanges irlba jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime mixsqp openssl pillar pkgconfig prettyunits progress purrr R6 Rcpp RcppArmadillo rlang S4Arrays S4Vectors SparseArray SQUAREM stringi stringr SummarizedExperiment sys tibble tidyr tidyselect truncnorm tzdb UCSC.utils utf8 vctrs vroom withr XVector zlibbioc

An introduction to the QTLExperiment class

Christina B Azodi, Amelia Dunstone, Davis McCarthy

Rendered fromQTLExperiment.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-02-21
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
Named colData getters and setters	qtle-col_ids state_id state_id,QTLExperiment-method state_id<- state_id<-,QTLExperiment-method
Combining QTLExperiment objects	cbind,QTLExperiment-method QTLe-combine rbind,QTLExperiment-method
Internal QTLExperiment functions	colData,QTLExperiment-method int_colData int_colData,QTLExperiment-method int_colData<- int_colData<-,QTLExperiment-method int_metadata int_metadata,QTLExperiment-method int_metadata<- int_metadata<-,QTLExperiment-method int_rowData int_rowData,QTLExperiment-method int_rowData<- int_rowData<-,QTLExperiment-method parallel_slot_names,QTLExperiment-method QTLe-internals rowData,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	QTLe-recover recover_qtle_ids
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
Subsetting and replacing data in QTLExperiment objects	QTLe-subset [,QTLExperiment,ANY,ANY,ANY-method [,QTLExperiment,ANY,ANY-method [,QTLExperiment,ANY-method [<-,QTLExperiment,ANY,ANY,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
Coerce QTL summary statistics into a QTLExperiment object	sumstats2qtle
Update a QTLExperiment object	updateObject updateObject,QTLExperiment-method