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genomicper
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]
[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 21 Nov. 2024.
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Complete documentation for genomicper
Functions, R codes and Examples using
the genomicper R package
Some associated functions: RHSAXXXXX . SNPsAnnotation . demo . genes_permutation . genome_order . genomicper-package . get_pathways . get_results . hyprbg . plot_results . read2_paths . read_pvals . snps_permutation .
Some associated R codes: genes_permutation.R . genome_order.R . get_pathways.R . get_results.R . hyprbg.R . plot_results.R . read2_paths.R . read_pvals.R . snps_permutation.R . Full genomicper package functions and examples
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