Package: BGData 2.4.1

Alexander Grueneberg

BGData: A Suite of Packages for Analysis of Big Genomic Data

An umbrella package providing a phenotype/genotype data structure and scalable and efficient computational methods for large genomic datasets in combination with several other packages: 'BEDMatrix', 'LinkedMatrix', and 'symDMatrix'.

Authors:Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre], Paulino Perez [ctb], Ana Vazquez [ctb]

BGData_2.4.1.tar.gz
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BGData_2.4.1.tgz(r-4.6-x86_64)BGData_2.4.1.tgz(r-4.6-arm64)BGData_2.4.1.tgz(r-4.5-x86_64)BGData_2.4.1.tgz(r-4.5-arm64)
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BGData_2.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BGData/json (API)
NEWS

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

Bug tracker:https://github.com/quantgen/bgdata/issues

Uses libs:
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

geneticsgenomicsgwasr-pkgopenmp

5.45 score 34 stars 55 scripts 334 downloads 3 mentions 23 exports 12 dependencies

Last updated from:fe7a57779d. Checks:11 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR176
linux-devel-x86_64ERROR165
source / vignettesOK178
linux-release-arm64ERROR136
linux-release-x86_64ERROR137
macos-release-arm64ERROR108
macos-release-x86_64ERROR279
macos-oldrel-arm64ERROR112
macos-oldrel-x86_64ERROR230
windows-develERROR112
windows-releaseERROR111
windows-oldrelERROR111
wasm-releaseOK115

Exports:as.BGDataBGDatachunkedApplychunkedMapfindRelatedFWDgenogeno<-getGgetG_symDMatrixGWASload.BGDatamapmap<-orderedMergephenopheno<-preprocessreadRAWreadRAW_big.matrixreadRAW_matrixsegmentssummarize

Dependencies:BEDMatrixBHbigmemorybigmemory.sribitcrochetffLinkedMatrixRcppsymDMatrixsynchronicityuuid

Readme and manuals

Help Manual

Help pageTopics
A Suite of Packages for Analysis of Big Genomic DataBGData-package
Convert Other Objects to BGData Objectsas.BGData as.BGData.BEDMatrix as.BGData.ColumnLinkedMatrix as.BGData.RowLinkedMatrix
Creates a New BGData InstanceBGData
Container for Phenotype and Genotype DataBGData-class geno,BGData-method geno<-,BGData-method map,BGData-method map<-,BGData-method pheno,BGData-method pheno<-,BGData-method
Applies a Function on Each Row or Column of a File-Backed MatrixchunkedApply
Applies a Function on Each Chunk of a File-Backed MatrixchunkedMap
File-Backed Matricesfile-backed-matrices
Find related individuals in a relationship matrixfindRelated findRelated.matrix findRelated.symDMatrix
Performs Forward RegressionsFWD
Getting/Setting Genotypes, Sample Information, and Variant Informationgeno geno<- map map<- pheno pheno<-
An Abstract S4 Class Union of Matrix-Like Typesgeno-class
Computes a Genomic Relationship MatrixgetG
Computes a Very Large Genomic Relationship MatrixgetG_symDMatrix
Performs Single Marker Regressions Using BGData ObjectsGWAS
Loads BGData (and Other) Objects from .RData Filesload.BGData
Multi-Level Parallelismmulti-level-parallelism
Merge Two Data Frames Keeping the Order of the FirstorderedMerge
Center, scale, and impute datapreprocess
Creates a BGData Object From a .raw File or a .ped-Like FilereadRAW readRAW_big.matrix readRAW_matrix
Find non-overlapping segments based on a summary statisticsegments
Generates Various Summary Statisticssummarize