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

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

Peer review:

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

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

On CRAN:

geneticsgenomicsgwasr-pkg

5.34 score 34 stars 43 scripts 459 downloads 3 mentions 23 exports 12 dependencies

Last updated 1 years agofrom:fc1cda1987. Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-win-x86_64ERRORNov 12 2024
R-4.5-linux-x86_64ERRORNov 12 2024
R-4.4-win-x86_64ERRORNov 12 2024
R-4.4-mac-x86_64ERRORNov 12 2024
R-4.4-mac-aarch64ERRORNov 12 2024
R-4.3-win-x86_64ERRORNov 12 2024
R-4.3-mac-x86_64ERRORNov 12 2024
R-4.3-mac-aarch64ERRORNov 12 2024

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