hap
(Package: gap) :
Haplotype reconstruction
Haplotype reconstruction using sorting and trimming algorithms
● Data Source:
CranContrib
● Keywords: models
● Alias: hap
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pbsize
(Package: gap) :
Power for population-based association design
This function implements Long et al. (1997) statistics for population-based association design. This is based on a contingency table test and accurate level of significance can be obtained by Fisher's exact test.
● Data Source:
CranContrib
● Keywords: misc
● Alias: pbsize
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masize
(Package: gap) :
Sample size calculation for mediation analysis
The function computes sample size for regression problems where the goal is to assess mediation of the effects of a primary predictor by an intermediate variable or mediator.
● Data Source:
CranContrib
● Keywords: misc
● Alias: masize
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gcontrol2
(Package: gap) :
genomic control based on p values
The function obtains 1-df chi-squared statistics (observed) according to a vector of p values, and the inflation factor (lambda) according to medians of the observed and expected statistics. The latter is based on the empirical distribution function (EDF) of 1-df chi-squared statstics.
● Data Source:
CranContrib
● Keywords: models
● Alias: gcontrol2
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hwe.cc
(Package: gap) :
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
● Data Source:
CranContrib
● Keywords: htest
● Alias: hwe.cc
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gif
(Package: gap) :
Kinship coefficient and genetic index of familiality
The genetic index of familality is defined as the mean kinship between all pairs of individuals in a set multiplied by 100,000. Formally, it is defined as
● Data Source:
CranContrib
● Keywords: datagen
● Alias: gif
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fbsize
(Package: gap) :
Sample size for family-based linkage and association design
This function implements Risch and Merikangas (1996) statistics evaluating power for family-based linkage (affected sib pairs, ASP) and association design. They are potentially useful in the prospect of genome-wide association studies.
● Data Source:
CranContrib
● Keywords: misc
● Alias: fbsize
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ESplot
(Package: gap) :
Effect-size plot
The function accepts parameter estimates and their standard errors for a range of models.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: ESplot
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BFDP
(Package: gap) :
Bayesian false-discovery probability
This function calculates BFDP, the approximate Pr( H0 | thetahat ), given an estiamte of the log relative risk, thetahat, the variance of this estimate, V, the prior variance, W, and the prior probability of a non-null association. When logscale=TRUE, the function accepts an estimate of the relative risk, RRhat, and the upper point of a 95% confidence interval RRhi.
● Data Source:
CranContrib
● Keywords: models
● Alias: BFDP
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b2r
(Package: gap) :
Obtain correlation coefficients and their variance-covariances
This function converts linear regression coefficients of phenotype on single nucleotide polymorphisms (SNPs) into Pearson correlation coefficients with their variance-covariance matrix. It is useful as a preliminary step for meta-analyze SNP-trait associations at a given region. Between-SNP correlations (e.g., from HapMap) are required as auxiliary information.
● Data Source:
CranContrib
● Keywords: datagen
● Alias: b2r
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