genomicper: Circular Genomic Permutation using Gwas p-Values of Association
Version 1.6

Circular genomic permutation approach uses GWAS results to establish the significance of pathway/gene-set associations whilst accounting for genomic structure. All 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. The SNPs annotation and pathways annotations can be performed within the package or provided by the user.

AuthorClaudia P. Cabrera, Pau Navarro, Chris S.Haley
Date of publication2016-07-05 23:42:23
MaintainerClaudia Cabrera <c.cabrera@qmul.ac.uk>
LicenseGPL-2
Version1.6
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("genomicper")

Getting started

Package overview

Popular man pages

demo: GWAS p_values demo data
genomicper-package: Circular Genomic Permutations
get_results: Circular Permutation Results
hsaXXXXX: KEGG pathways examples
hyprbg: Hypergeometric Test (phyper)
SNPsAnnotation: SNPs-Genes annotation to Distance 0 (SNPs within a gene)
snps_permutation: SNP-level permutations
See all...

All man pages Function index File listing

Man pages

demo: GWAS p_values demo data
genes_permutation: Gene-level Permutations
genome_order: Genome Order
genomicper-package: Circular Genomic Permutations
get_pathways: Pathways
get_results: Circular Permutation Results
hsaXXXXX: KEGG pathways examples
hyprbg: Hypergeometric Test (phyper)
plot_results: Plot Results Circular Permutation
read2_paths: Read to SNPs to sets; Map SNPs to gene-sets/pathways
read_pvals: Read GWAS p-values of association and Merge with SNP...
SNPsAnnotation: SNPs-Genes annotation to Distance 0 (SNPs within a gene)
snps_permutation: SNP-level permutations

Functions

SNPsAnnotation Man page
demo Man page
genes_permutation Man page Source code
genome_order Man page Source code
genomicper Man page
genomicper-package Man page
get_pathways Man page Source code
get_results Man page Source code
hsa00100 Man page
hsa00120 Man page
hsa00130 Man page
hsa00140 Man page
hsa00190 Man page
hsa02010 Man page
hsaXXXXX Man page
hyprbg Man page Source code
plot_results Man page Source code
read2_paths Man page Source code
read_pvals Man page Source code
snps_permutation Man page Source code

Files

NAMESPACE
data
data/hsa00100.rda
data/hsa00120.rda
data/demo.rda
data/hsa02010.rda
data/SNPsAnnotation.rda
data/hsa00190.rda
data/hsa00140.rda
data/hsa00130.rda
R
R/get_results.R
R/read2_paths.R
R/genome_order.R
R/hyprbg.R
R/genes_permutation.R
R/plot_results.R
R/snps_permutation.R
R/get_pathways.R
R/read_pvals.R
MD5
DESCRIPTION
man
man/genomicper-package.Rd
man/demo.Rd
man/snps_permutation.Rd
man/plot_results.Rd
man/read_pvals.Rd
man/genes_permutation.Rd
man/hsaXXXXX.Rd
man/SNPsAnnotation.Rd
man/hyprbg.Rd
man/genome_order.Rd
man/get_results.Rd
man/read2_paths.Rd
man/get_pathways.Rd
genomicper documentation built on May 19, 2017, 8:39 a.m.

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