Circular Genomic Permutation using Genome Wide Association
p-Values
c(person(given=c("Claudia","P"),family="Cabrera",role = c("aut", "cre"),
email = "c.cabrera@qmul.ac.uk"),
person(given="Pau",family="Navarro", role = "aut"),
person(given=c("Chris","S"),family="Haley", role = "aut"))
Claudia P Cabrera [aut, cre],
Pau Navarro [aut],
Chris S Haley [aut]
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.

c(person(given=c("Stephen", "Alfred"), family="Sefick", email = "ssefick@gmail.com", role = c("aut", "cre")), person(given=c("Magdelena", "A"),family="Castronova", email = "mac0079@auburn.edu", role = c("aut")), person(given=c("Laurie", "S"), family="Stevison", email = "lss0021@auburn.edu", role = c("aut")))
We implement a common genotyping workflow with a standardized software interface. 'genotypeR' designs genotyping markers from vcf files, outputs markers for multiplexing suitability on various platforms (Sequenom and Illumina GoldenGate), and provides various QA/QC and analysis functions. We developed this package to analyze data in Stevison LS, SA Sefick, CA Rushton, and RM Graze. Accepted. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci. <DOI:10.1098/rstb.2015.0615>.
The SequenomMarkers() marker design function
requires 'vcftools' and 'Perl' on 'windows', and, in addition,
'awk' and 'bash' on '*nix'.
methods, reshape2, plyr, doBy, zoo, colorspace
Stephen Alfred Sefick [aut, cre],
Magdelena A Castronova [aut],
Laurie S Stevison [aut]