MCPerm: A Monte Carlo permutation method for multiple test correlation

A Monte Carlo permutation method for multiple test correlation.

Author
Lanying Zhang and Yongshuai Jiang
Date of publication
2013-06-17 16:58:49
Maintainer
Yongshuai Jiang <jiangyongshuai@gmail.com>
License
GPL-2
Version
1.1.4

View on CRAN

Man pages

Armitage
Armitage's trend test for the 2x3 genotype table
Armitage.MCPerm
A Monte Carlo permutation method for Armitage's trend test in...
Armitage.TradPerm
A permutation method for Armitage's trend test in...
chisq.MCPerm
A Monte Carlo permutation method for multiple chisq.test...
chisq.TradPerm
A permutation test for multiple chisq.test correction in...
fisher.MCPerm
A Monte Carlo permutation method for multiple fisher.test...
fisher.TradPerm
A permutation test for multiple fisher.test correction in...
genotypeData
Genotype Data from GWA16
genotypeStat
Statistical Allele and Genotype Frequency of the specified...
HW.test
Hardy-weinberg equilibrium test
I2.MCPerm
Calculate p.value for Heterogeneity statistics I2 in meta...
I2.TradPerm
Calculate p.value for Heterogeneity statistics I2 in meta...
MCPerm-package
A Monte Carlo permutation method for multiple test...
meta
Meta analysis
MetaGenotypeCount
rs3131296 genetic association studies from SZGene database
MetaGenotypeData
genotype raw data for rs3131296 genetic association studies
meta.MCPerm
Meta analysis corrected by permutation test
meta.TradPerm
Meta analysis corrected by permutation test
OR
OR(odd ratio) for risk_allele
OR.MCPerm
A Monte Carlo permutation method for multiple OR(odd ratio)...
OR.TradPerm
A permutation test for multiple OR(odd ratio) test correction...
pearson_scatter
scatter plot and calculate Pearson correlation coefficient...
PermMeta.boxplot
boxplot for the result of 'meta.MCPerm' or 'meta.TradPerm'
PermMeta.Hist
histplot for the result of 'meta.MCPerm' or 'meta.TradPerm'
PermMeta.LnOR.boxplot
boxplot for the return value 'perm_LnOR' or 'perm_VARLnOR' of...
PermMeta.LnOR.CDC
cumulative distribution curve for the return value...
PermMeta.LnOR.Hist
histplot for the return value 'perm_LnOR' or 'perm_VARLnOR'...
PermMeta.LnOR.qqnorm
qqnorm plot for the return value 'perm_LnOR' of 'meta.MCPerm'...
permuteGenotype
Permute the elements of genotype data
permuteGenotypeCount
Fill the numerics of 2*3 table when fixed the row and column...
print.PermMeta
Print style for function 'meta.MCPerm' or 'meta.TradPerm'
Q.MCPerm
Correct p.value for Heterogeneity statistics Q in meta...
Q.TradPerm
Correct p.value for Heterogeneity statistics Q in meta...
VS.Allele.CDC
separately plot cumulative distribution curve for the return...
VS.Allele.Hist
separately plot histplot for the return value(allele count)...
VS.Allele.QQ
separately plot quantile-quantile plot for the return...
VS.CDC
plot cumulative distribution curve for the return value of...
VS.Genotype.CDC
separately plot cumulative distribution curve for the return...
VS.Genotype.Hist
separately plot histplot for the return value(genotype count)...
VS.Genotype.QQ
separately plot quantile-quantile plot for the return...
VS.Hist
plot histplot for the return value of 'meta.TradPerm' and...
VS.KS
Kolmogorov-Smirnov test for the return value of...
VS.QQ
plot quantile-quantile plot for the return value of...

Files in this package

MCPerm
MCPerm/MD5
MCPerm/NAMESPACE
MCPerm/DESCRIPTION
MCPerm/data
MCPerm/data/MetaGenotypeData.rda
MCPerm/data/MetaGenotypeCount.rda
MCPerm/data/genotypeData.rda
MCPerm/man
MCPerm/man/VS.QQ.Rd
MCPerm/man/VS.KS.Rd
MCPerm/man/VS.Hist.Rd
MCPerm/man/VS.Genotype.QQ.Rd
MCPerm/man/VS.Genotype.Hist.Rd
MCPerm/man/VS.Genotype.CDC.Rd
MCPerm/man/VS.CDC.Rd
MCPerm/man/VS.Allele.QQ.Rd
MCPerm/man/VS.Allele.Hist.Rd
MCPerm/man/VS.Allele.CDC.Rd
MCPerm/man/Q.TradPerm.Rd
MCPerm/man/Q.MCPerm.Rd
MCPerm/man/print.PermMeta.Rd
MCPerm/man/permuteGenotypeCount.Rd
MCPerm/man/permuteGenotype.Rd
MCPerm/man/PermMeta.LnOR.qqnorm.Rd
MCPerm/man/PermMeta.LnOR.Hist.Rd
MCPerm/man/PermMeta.LnOR.CDC.Rd
MCPerm/man/PermMeta.LnOR.boxplot.Rd
MCPerm/man/PermMeta.Hist.Rd
MCPerm/man/PermMeta.boxplot.Rd
MCPerm/man/pearson_scatter.Rd
MCPerm/man/OR.TradPerm.Rd
MCPerm/man/OR.MCPerm.Rd
MCPerm/man/OR.Rd
MCPerm/man/MetaGenotypeData.Rd
MCPerm/man/MetaGenotypeCount.Rd
MCPerm/man/meta.TradPerm.Rd
MCPerm/man/meta.MCPerm.Rd
MCPerm/man/meta.Rd
MCPerm/man/I2.TradPerm.Rd
MCPerm/man/I2.MCPerm.Rd
MCPerm/man/HW.test.Rd
MCPerm/man/genotypeStat.Rd
MCPerm/man/genotypeData.Rd
MCPerm/man/fisher.TradPerm.Rd
MCPerm/man/fisher.MCPerm.Rd
MCPerm/man/chisq.TradPerm.Rd
MCPerm/man/chisq.MCPerm.Rd
MCPerm/man/Armitage.TradPerm.Rd
MCPerm/man/Armitage.MCPerm.Rd
MCPerm/man/Armitage.Rd
MCPerm/man/MCPerm-package.Rd
MCPerm/R
MCPerm/R/VS.QQ.R
MCPerm/R/VS.KS.R
MCPerm/R/VS.Hist.R
MCPerm/R/VS.Genotype.QQ.R
MCPerm/R/VS.Genotype.Hist.R
MCPerm/R/VS.Genotype.CDC.R
MCPerm/R/VS.CDC.R
MCPerm/R/VS.Allele.QQ.R
MCPerm/R/VS.Allele.Hist.R
MCPerm/R/VS.Allele.CDC.R
MCPerm/R/Q.TradPerm.R
MCPerm/R/Q.MCPerm.R
MCPerm/R/print.PermMeta.R
MCPerm/R/permuteGenotypeCount.R
MCPerm/R/permuteGenotype.R
MCPerm/R/PermMeta.LnOR.qqnorm.R
MCPerm/R/PermMeta.LnOR.Hist.R
MCPerm/R/PermMeta.LnOR.CDC.R
MCPerm/R/PermMeta.LnOR.boxplot.R
MCPerm/R/PermMeta.Hist.R
MCPerm/R/PermMeta.boxplot.R
MCPerm/R/pearson_scatter.R
MCPerm/R/OR.TradPerm.R
MCPerm/R/OR.MCPerm.R
MCPerm/R/OR.R
MCPerm/R/meta.TradPerm.R
MCPerm/R/meta.MCPerm.R
MCPerm/R/meta.R
MCPerm/R/I2.TradPerm.R
MCPerm/R/I2.MCPerm.R
MCPerm/R/HW.test.R
MCPerm/R/genotypeStat.R
MCPerm/R/fisher.TradPerm.R
MCPerm/R/fisher.MCPerm.R
MCPerm/R/chisq.TradPerm.R
MCPerm/R/chisq.MCPerm.R
MCPerm/R/Armitage.TradPerm.R
MCPerm/R/Armitage.MCPerm.R
MCPerm/R/Armitage.R