ASAFE
Bioc currentAncestry Specific Allele Frequency Estimation
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
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.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
17 0 exported
Complexity
3.5 avg / 31 max
Call network
17 nodes / 14 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,788
Files
49
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
17
Testing & CI
Has tests
Yes
Test-to-code ratio
0.56
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
0%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.2
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- References docs
- 50%
Topics
People
Qian Zhang
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ASAFE")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.