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MCPerm (version 1.1.4)

A Monte Carlo permutation method for multiple test correlation

Description

A Monte Carlo permutation method for multiple test correlation.

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Version

Install

install.packages('MCPerm')

Monthly Downloads

14

Version

1.1.4

License

GPL-2

Maintainer

Yongshuai Jiang

Last Published

June 17th, 2013

Functions in MCPerm (1.1.4)

chisq.MCPerm

A Monte Carlo permutation method for multiple chisq.test correction in case/control association study
genotypeStat

Statistical Allele and Genotype Frequency of the specified snp
fisher.TradPerm

A permutation test for multiple fisher.test correction in case/control association study
chisq.TradPerm

A permutation test for multiple chisq.test correction in case/control association study
genotypeData

Genotype Data from GWA16
HW.test

Hardy-weinberg equilibrium test
Armitage

Armitage's trend test for the 2x3 genotype table
fisher.MCPerm

A Monte Carlo permutation method for multiple fisher.test correction in case/control association study
Armitage.MCPerm

A Monte Carlo permutation method for Armitage's trend test in case/control association study
Armitage.TradPerm

A permutation method for Armitage's trend test in case/control association study
I2.MCPerm

Calculate p.value for Heterogeneity statistics I2 in meta analysis
MetaGenotypeCount

rs3131296 genetic association studies from SZGene database
meta.MCPerm

Meta analysis corrected by permutation test
MetaGenotypeData

genotype raw data for rs3131296 genetic association studies
OR

OR(odd ratio) for risk_allele
OR.MCPerm

A Monte Carlo permutation method for multiple OR(odd ratio) test correction in case/control association study
MCPerm-package

A Monte Carlo permutation method for multiple test correction.
I2.TradPerm

Calculate p.value for Heterogeneity statistics I2 in meta analysis
meta

Meta analysis
meta.TradPerm

Meta analysis corrected by permutation test
permuteGenotypeCount

Fill the numerics of 2*3 table when fixed the row and column totals
PermMeta.LnOR.boxplot

boxplot for the return value 'perm_LnOR' or 'perm_VARLnOR' of 'meta.MCPerm' or 'meta.TradPerm'
Q.TradPerm

Correct p.value for Heterogeneity statistics Q in meta analysis by TradPerm method
VS.Allele.CDC

separately plot cumulative distribution curve for the return value(allele count) of 'meta.TradPerm' and 'meta.MCPerm' for certain study
VS.Hist

plot histplot for the return value of 'meta.TradPerm' and 'meta.MCPerm' for certain study or meta analysis
VS.KS

Kolmogorov-Smirnov test for the return value of 'meta.TradPerm' and 'meta.MCPerm'
permuteGenotype

Permute the elements of genotype data
PermMeta.LnOR.CDC

cumulative distribution curve for the return value 'perm_LnOR' of 'meta.MCPerm' or 'meta.TradPerm'
PermMeta.boxplot

boxplot for the result of 'meta.MCPerm' or 'meta.TradPerm'
PermMeta.Hist

histplot for the result of 'meta.MCPerm' or 'meta.TradPerm'
VS.Allele.Hist

separately plot histplot for the return value(allele count) of 'meta.TradPerm' and 'meta.MCPerm' for certain study
VS.QQ

plot quantile-quantile plot for the return value of 'meta.TradPerm' and 'meta.MCPerm' for certain study or meta analysis.
VS.Allele.QQ

separately plot quantile-quantile plot for the return value(allele count) of 'meta.TradPerm' and 'meta.MCPerm' for certain study
OR.TradPerm

A permutation test for multiple OR(odd ratio) test correction in case/control association study
pearson_scatter

scatter plot and calculate Pearson correlation coefficient for paired data
print.PermMeta

Print style for function 'meta.MCPerm' or 'meta.TradPerm'
Q.MCPerm

Correct p.value for Heterogeneity statistics Q in meta analysis by MCPerm method.
VS.Genotype.Hist

separately plot histplot for the return value(genotype count) of 'meta.TradPerm' and 'meta.MCPerm' for certain study
PermMeta.LnOR.Hist

histplot for the return value 'perm_LnOR' or 'perm_VARLnOR' of 'meta.MCPerm' or 'meta.TradPerm'
VS.Genotype.QQ

separately plot quantile-quantile plot for the return value(genotype count) of 'meta.TradPerm' and 'meta.MCPerm' for certain study
PermMeta.LnOR.qqnorm

qqnorm plot for the return value 'perm_LnOR' of 'meta.MCPerm' or 'meta.TradPerm'
VS.CDC

plot cumulative distribution curve for the return value of 'meta.TradPerm' and 'meta.MCPerm' for certain study or meta analysis
VS.Genotype.CDC

separately plot cumulative distribution curve for the return value(genotype count) of 'meta.TradPerm' and 'meta.MCPerm' for certain study