Introduction: What ASAFE does | ASAFE in the Context of a Larger Genetic Analysis Workflow | Input Files | Ancestry File | Rows | Columns | Entries | Genotype File | Functions | Reproducibility | Try ASAFE Out on a Small Data Set | Citation
Package: ASAFE 1.39.0
Qian Zhang
ASAFE: Ancestry Specific Allele Frequency Estimation
Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.
Authors:
ASAFE_1.39.0.tar.gz
ASAFE_1.39.0.zip(r-4.7)ASAFE_1.39.0.zip(r-4.6)ASAFE_1.39.0.zip(r-4.5)
ASAFE_1.39.0.tgz(r-4.6-any)ASAFE_1.39.0.tgz(r-4.5-any)
ASAFE_1.39.0.tar.gz(r-4.7-any)ASAFE_1.39.0.tar.gz(r-4.6-any)
ASAFE_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ASAFE/json (API)
| # Install 'ASAFE' in R: |
| install.packages('ASAFE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- adm_ancestries_test - Ancestries of 250 admixed individuals at 6 SNPs
- adm_genotypes_test - Genotypes of 250 admixed individuals at 6 markers
On BioConductor:ASAFE-1.39.0(bioc 3.24)ASAFE-1.38.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
snpgenomewideassociationlinkagedisequilibriumbiomedicalinformaticsgeneticsexperimentaldesign
Last updated from:1324a93673. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 133 | ||
| linux-devel-x86_64 | OK | 140 | ||
| source / vignettes | OK | 170 | ||
| linux-release-x86_64 | OK | 193 | ||
| macos-release-arm64 | OK | 71 | ||
| macos-oldrel-arm64 | OK | 97 | ||
| windows-devel | OK | 83 | ||
| windows-release | OK | 62 | ||
| windows-oldrel | OK | 67 | ||
| wasm-release | OK | 104 |
Exports:algorithm_1snpalgorithm_1snp_wrapper
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Ancestries of 250 admixed individuals at 6 SNPs | adm_ancestries_test |
| Genotypes of 250 admixed individuals at 6 markers | adm_genotypes_test |
| Estimate ancestry-specific allele frequencies for 1 marker (e.g. a SNP) from individuals' alleles and ancestries at this marker. | algorithm_1snp |
| Wrapper for function algorithm_1snp | algorithm_1snp_wrapper |
