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AssocAFC
View on CRAN: Click
here
Download and install AssocAFC package within the R console
Install from CRAN:
install.packages("AssocAFC")
Install from Github:
library("remotes")
install_github("cran/AssocAFC") Install by package version:
library("remotes")
install_version("AssocAFC", "1.0.2") Attach the package and use:
library("AssocAFC")
Maintained by
Khalid B. Kunji
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-11-28
Latest Update:
Description:
When doing association analysis one does not always have the
genotypes for the control population. In such cases it may be
necessary to fall back on frequency based tests using well known sources
for the frequencies in the control population, for instance, from the
1000 Genomes Project. The Allele Frequency Comparison ('AssocAFC') package
performs multiple rare variant association analyses in both population and
family-based GWAS (Genome-Wide Association Study) designs. It includes
three score tests that are based on the difference of the sum of allele
frequencies between cases and controls. Two of these tests, Wcorrected()
and Wqls(), are collapsing-based tests and suffer from having protective
and risk variants. The third test, afcSKAT(), is a score test that
overcomes the mix of SNP (Single-Nucleotide Polymorphism) effect
directions. For more details see
Saad M and Wijsman EM (2017) .
How to cite:
Khalid B. Kunji (2017). AssocAFC: Allele Frequency Comparison. R package version 1.0.2, https://cran.r-project.org/web/packages/AssocAFC. Accessed 10 Oct. 2026.
Previous versions and publish date:
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Other R packages that AssocAFC depends,
imports, suggests or enhances
Complete documentation for AssocAFC
Functions, R codes and Examples using
the AssocAFC R package
Some associated functions: AssocAFC-package . Wcorrected . Wqls . afcSKAT . cor.afc . geno.afc . kin.afc . maf.afc . phenotype.afc . weights.afc .
Some associated R codes: Wcorrected.R . Wqls.R . afcSKAT.R . Full AssocAFC package functions and examples
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