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lfa

logistic factor analysis

https://github.com/storeylab/lfa

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ✓
    Committers with academic emails
    3 of 7 committers (42.9%) from academic institutions
  • ✓
    Institutional organization owner
    Organization storeylab has institutional domain (genomics.princeton.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.2%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

logistic factor analysis

Basic Info
  • Host: GitHub
  • Owner: StoreyLab
  • License: gpl-3.0
  • Language: R
  • Default Branch: devel
  • Size: 989 KB
Statistics
  • Stars: 16
  • Watchers: 7
  • Forks: 8
  • Open Issues: 1
  • Releases: 0
Created over 11 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

lfa

Logistic factor analysis

Installation

To install latest version on Bioconductor, open R and type:

```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("lfa") ```

You can also install development version from GitHub this way: R install.packages("devtools") library("devtools") install_github("Storeylab/lfa") Apple OS X users, see Troubleshooting below.

Data input

We recommend using the genio or BEDMatrix packages to read genotype data into an R matrix.

Be warned that genotype matrices from genio and some lfa functions require a lot of memory. As a rule of thumb, the in memory sizes of a few relevant genotype matrices:

  • 431345 SNPs by 940 individuals: 1.5 GB needed for genotype matrix, about 9 GB to run lfa.
  • 339100 SNPs by 1500 individuals: 1.9 GB needed for genotype matrix, about 11.5 GB to run lfa.

BEDMatrix inputs consume much less memory but can be slower otherwise.

Troubleshooting

Apple OS X users may experience a problem due to Fortran code that is included in this package. You must install the X code command line tools (XCode CLI) and gfortran. Try the following commands on terminal:

xcode-select --install brew install gcc

If XCode installation fails, you may have to sign up on Apple Developer: https://www.ics.uci.edu/~pattis/common/handouts/macmingweclipse/allexperimental/macxcodecommandlinetools.html

Alternatively, this Installer Package for macOS R toolchain may work https://github.com/rmacoslib/r-macos-rtools/

Citations

Hao, Wei, Minsun Song, and John D. Storey. "Probabilistic Models of Genetic Variation in Structured Populations Applied to Global Human Studies." Bioinformatics 32, no. 5 (March 1, 2016): 713–21. doi:10.1093/bioinformatics/btv641. arXiv.

Owner

  • Name: Storey Lab
  • Login: StoreyLab
  • Kind: organization
  • Location: Princeton, NJ USA

Storey Lab at Princeton University

GitHub Events

Total
  • Push event: 2
  • Create event: 2
Last Year
  • Push event: 2
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 59
  • Total Committers: 7
  • Avg Commits per committer: 8.429
  • Development Distribution Score (DDS): 0.542
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Wei Hao w****o@p****u 27
Alejandro Ochoa Garcia a****g@g****m 15
Wei Hao w****o@g****U 8
ncchung n****g@g****m 3
Neo Christopher Chung n****g 3
John D. Storey j****y 2
Wei Hao w****o@h****u 1
Committer Domains (Top 20 + Academic)
hex.princeton.edu: 1 gen-whao-cuda.princeton.edu: 1 princeton.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 3
  • Total pull requests: 3
  • Average time to close issues: about 19 hours
  • Average time to close pull requests: 1 day
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 2.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ajbass (1)
  • starsareintherose (1)
  • jhmarcus (1)
Pull Request Authors
  • ncchung (2)
  • alexviiia (1)
Top Labels
Issue Labels
question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 50,308 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: lfa

Logistic Factor Analysis for Categorical Data

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 50,308 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 5.6%
Average: 6.9%
Stargazers count: 8.7%
Downloads: 20.4%
Maintainers (1)
alejandro.ochoa@duke.edu
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • RSpectra * imports
  • corpcor * imports
  • methods * imports
  • utils * imports
  • BEDMatrix * suggests
  • genio * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • testthat * suggests