Package: genomicper 1.7

Claudia P Cabrera

genomicper: Circular Genomic Permutation using Genome Wide Association p-Values

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) <doi:10.1534/g3.112.002618>). 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.

Authors:Claudia P Cabrera [aut, cre], Pau Navarro [aut], Chris S Haley [aut]

genomicper_1.7.tar.gz
genomicper_1.7.tar.gz(r-4.5-noble)genomicper_1.7.tar.gz(r-4.4-noble)
genomicper_1.7.tgz(r-4.4-emscripten)genomicper_1.7.tgz(r-4.3-emscripten)
genomicper.pdf |genomicper.html
genomicper/json (API)

# Install 'genomicper' in R:
install.packages('genomicper', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.15 score 1 stars 14 scripts 536 downloads 1 mentions 9 exports 40 dependencies

Last updated 4 years agofrom:a87250a9d5. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-linuxOKNov 21 2024

Exports:genes_permutationgenome_orderget_pathwaysget_resultshyprbgplot_resultsread_pvalsread2_pathssnps_permutation

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6reactome.dbrlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc