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:
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')) |
- RHSA109582 - Reactome Pathway examples
- RHSA1474244 - Reactome Pathway examples
- RHSA164843 - Reactome Pathway examples
- RHSA446343 - Reactome Pathway examples
- RHSA8876384 - Reactome Pathway examples
- RHSA8964572 - Reactome Pathway examples
- SNPsAnnotation - SNPs-Genes annotation to Distance 0
- demo - GWAS p_values demo data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:a87250a9d5. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 22 2024 |
R-4.5-linux | OK | Oct 22 2024 |
Exports:genes_permutationgenome_orderget_pathwaysget_resultshyprbgplot_resultsread_pvalsread2_pathssnps_permutation
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6reactome.dbrlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Circular Genomic Permutations | genomicper-package genomicper |
GWAS p_values demo data | demo |
Gene-level Permutations | genes_permutation |
Genome Order | genome_order |
Pathways | get_pathways |
Circular Permutation Results | get_results |
Hypergeometric Test (phyper) | hyprbg |
Plot Results Circular Permutation | plot_results |
Read GWAS p-values of association and Merge with SNP annotations | read_pvals |
Read to SNPs to sets; Map SNPs to gene-sets/pathways | read2_paths |
Reactome Pathway examples | RHSA109582 RHSA1474244 RHSA164843 RHSA446343 RHSA8876384 RHSA8964572 RHSAXXXXX |
SNP-level permutations | snps_permutation |
SNPs-Genes annotation to Distance 0 (SNPs within a gene) | SNPsAnnotation |