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AssocAFC  

Allele Frequency Comparison
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]
All associated links for this package
First Published: 2017-11-28
Latest Update: 2018-05-05
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 08 May. 2025.
Previous versions and publish date:
1.0.1 (2017-11-28 19:30), 1.0.2 (2018-05-05 11:34)
Other packages that cited AssocAFC R package
View AssocAFC citation profile
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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