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genomicper  

Circular Genomic Permutation using Genome Wide Association p-Values
View on CRAN: Click here


Download and install genomicper package within the R console
Install from CRAN:
install.packages("genomicper")

Install from Github:
library("remotes")
install_github("cran/genomicper")

Install by package version:
library("remotes")
install_version("genomicper", "1.7")



Attach the package and use:
library("genomicper")
Maintained by
Claudia P Cabrera
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2012-05-29
Latest Update: 2021-05-08
Description:
Circular genomic permutation approach uses genome wide association studies (GWAS) results to establish the significance of pathway/gene-set associations whilst accounting for genomic structure(Cabrera et al (2012) ). All single nucleotide polymorphisms (SNPs) in the GWAS are placed in a 'circular genome' according to their location. Then the complete set of SNP association p-values are permuted by rotation with respect to the SNPs' genomic locations. Two testing frameworks are available: permutations at the gene level, and permutations at the SNP level. The permutation at the gene level uses Fisher's combination test to calculate a single gene p-value, followed by the hypergeometric test. The SNP count methodology maps each SNP to pathways/gene-sets and calculates the proportion of SNPs for the real and the permutated datasets above a pre-defined threshold. Genomicper requires a matrix of GWAS association p-values and SNPs annotation to genes. Pathways can be obtained from within the package or can be provided by the user.
How to cite:
Claudia P Cabrera (2012). genomicper: Circular Genomic Permutation using Genome Wide Association p-Values. R package version 1.7, https://cran.r-project.org/web/packages/genomicper. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.3 (2012-05-29 22:09), 1.6 (2016-07-05 23:42)
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