This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.
|Author||Juan R Gonzlez, Llus Armengol, Elisabet Guin, Xavier Sol, and Vctor Moreno|
|Date of publication||2014-04-23 09:27:48|
|Maintainer||Juan R Gonzlez <email@example.com>|
|License||GPL (>= 2)|
association: Association analysis between a single SNP and a given...
BonferroniSig: Bonferroni correction of p values
GenomicControl: Population substructure
getSignificantSNPs: Extract significant SNPs from an object of class...
haplointeraction: Haplotype interaction with a covariate
HapMap: SNPs from HapMap project
inheritance: Collapsing (or recoding) genotypes into different categories...
int: Identify interaction term
interactionPval: Two-dimensional SNP analysis for association studies
intervals: Print ORs and 95% confidence intervals for an object of class...
isMonomorphic: Check whether a SNP is Monomorphic
LD: max-statistic for a 2x3 table
makegeno: Create a group of locus objects from some SNPs, assign to...
maxstat: max-statistic for a 2x3 table
odds: Extract odds ratios, 95% CI and pvalues
permTest: Permutation test analysis
plotMissing: Plot of missing genotypes
plotWGassociation: Function to plot -log p values from an object of class...
qqpval: Functions for inspecting population substructure
scanWGassociation: Whole genome association analysis
setupSNP: Convert columns in a dataframe to class 'snp'
snp: SNP object
SNPassoc-internal: Internal SNPstat functions
SNPs: SNPs in a case-control study
sortSNPs: Sort a vector of SNPs by genomic position
tableHWE: Test for Hardy-Weinberg Equilibrium
Tablemeanse: Descriptive sample size, mean, and standard error
TableNPer: Descriptive sample size and percentage
WGassociation: Whole genome association analysis