permutation.snp
(Package: PIGE) :
Parallel computing of the Likelihhod ratio test (or Wald test) for an interaction term (or a simple SNP effect) on permutation sample
The permutation.snp function performs on permutation sample a Likelihood Ratio Test (or a Wald test) for an interaction term SNP*E (where E is an Environment variable) or for the effect of the SNP. This function uses the parallel computing on different CPU of the computer. This function returns a matrix containing for each permutation and SNP the p-value of the interaction term tested (SNP*E) or the p-value of the SNP effect tested.
● Data Source:
CranContrib
● Keywords:
● Alias: permutation.snp
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LR.cont
(Package: PIGE) :
Wald test for an adjusted model.
The LR.cont function performs a Wald test for a SNP effect. The function returns the p-value of the Wald test. It is an Internal function used by the permutation.snp function.
● Data Source:
CranContrib
● Keywords:
● Alias: LR.cont
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permutation.wrapper.cat.inter.Y.and.X
(Package: PIGE) :
Internal function used for the parallel computation on the permutation sample
Internal function used for the parallel computation on the permutation sample
● Data Source:
CranContrib
● Keywords: internal
● Alias: permutation.wrapper.cat.inter.Y.and.X
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LR.inter.cat.surv
(Package: PIGE) :
Likelihhod ratio test for an interaction term
The LR.inter.cat.surv function performs a likelihood ratio test (LRT) for an interaction term between a categorical variable and a SNP (coded 0,1,2) in a cox model. The function returns the p-value of the likelihood ratio test.
● Data Source:
CranContrib
● Keywords:
● Alias: LR.inter.cat.surv
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The data.to.list.gene.snp function generates the list containing for each gene the corresponding SNP ids from a txt file containing the SNP/gene annotation data. This list is required for the functions data.to.PIGE and ARTP.GE.
● Data Source:
CranContrib
● Keywords:
● Alias: data.to.list.gene.snp
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permutation.wrapper.cont.inter
(Package: PIGE) :
Internal function used for the parallel computation on the permutation sample
Internal function used for the parallel computation on the permutation sample
● Data Source:
CranContrib
● Keywords: internal
● Alias: permutation.wrapper.cont.inter
●
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permutation.wrapper.cont.inter.Y.and.X
(Package: PIGE) :
Internal function used for the parallel computation on the permutation sample
Internal function used for the parallel computation on the permutation sample
● Data Source:
CranContrib
● Keywords: internal
● Alias: permutation.wrapper.cont.inter.Y.and.X
●
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LR.cont.surv
(Package: PIGE) :
Wald test for an adjusted model.
The LR.cont.surv function performs a Wald test for a SNP effect based on a cox model. The function returns the p-value of the Wald test. It is an Internal function used by the permutation.snp function.
● Data Source:
CranContrib
● Keywords:
● Alias: LR.cont.surv
●
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permutation.wrapper.cont
(Package: PIGE) :
Internal function used for the parallel computation on the permutation sample
Internal function used for the parallel computation on the permutation sample
● Data Source:
CranContrib
● Keywords: internal
● Alias: permutation.wrapper.cont
●
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permutation.wrapper.cont.Y.and.X
(Package: PIGE) :
Internal function used for the parallel computation on the permutation sample
Internal function used for the parallel computation on the permutation sample
● Data Source:
CranContrib
● Keywords: internal
● Alias: permutation.wrapper.cont.Y.and.X
●
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