Package: Eagle 2.5
Andrew George
Eagle: Multiple Locus Association Mapping on a Genome-Wide Scale
An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Authors:
Eagle_2.5.tar.gz
Eagle_2.5.tar.gz(r-4.5-noble)Eagle_2.5.tar.gz(r-4.4-noble)
Eagle.pdf |Eagle.html✨
Eagle/json (API)
NEWS
| # Install 'Eagle' in R: |
| install.packages('Eagle', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/eagle
Last updated 3 years agofrom:593dd7f6bb. Checks:OK: 1 NOTE: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 07 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 07 2024 |
Exports:AMFPR4AMOpenGUIPlotAMReadMapReadMarkerReadPhenoReadZmatSummaryAM
Dependencies:askpassbase64encbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggthemesgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemmapmunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsassscalesshinyshinyBSshinyFilesshinyjsshinythemessourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Eagle for Genome-wide Association Mapping | Eagle-package Eagle |
| multiple-locus Association Mapping | AM |
| Set the false positive rate for 'AM' | FPR4AM |
| Browser-based Graphical User Interface | OpenGUI |
| Visualisation of multiple locus association mapping results | PlotAM |
| Read map file | ReadMap |
| Read marker data. | ReadMarker |
| Read phenotype file | ReadPheno |
| Read Z matrix | ReadZmat |
| Summary of multiple locus association mapping results | SummaryAM |
