MCPerm: A Monte Carlo permutation method for multiple test correlation

A Monte Carlo permutation method for multiple test correlation.

Install the latest version of this package by entering the following in R:
install.packages("MCPerm")
AuthorLanying Zhang and Yongshuai Jiang
Date of publication2013-06-17 16:58:49
MaintainerYongshuai Jiang <jiangyongshuai@gmail.com>
LicenseGPL-2
Version1.1.4

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...

Functions

Armitage Man page
Armitage.MCPerm Man page
Armitage.TradPerm Man page
chisq.MCPerm Man page
chisq.TradPerm Man page
fisher.MCPerm Man page
fisher.TradPerm Man page
genotypeData Man page
genotypeStat Man page
HW.test Man page
I2.MCPerm Man page
I2.TradPerm Man page
MCPerm Man page
MCPerm-package Man page
meta Man page
MetaGenotypeCount Man page
MetaGenotypeData Man page
meta.MCPerm Man page
meta.TradPerm Man page
OR Man page
OR.MCPerm Man page
OR.TradPerm Man page
pearson_scatter Man page
PermMeta.boxplot Man page
PermMeta.Hist Man page
PermMeta.LnOR.boxplot Man page
PermMeta.LnOR.CDC Man page
PermMeta.LnOR.Hist Man page
PermMeta.LnOR.qqnorm Man page
permuteGenotype Man page
permuteGenotypeCount Man page
print.PermMeta Man page
Q.MCPerm Man page
Q.TradPerm Man page
VS.Allele.CDC Man page
VS.Allele.Hist Man page
VS.Allele.QQ Man page
VS.CDC Man page
VS.Genotype.CDC Man page
VS.Genotype.Hist Man page
VS.Genotype.QQ Man page
VS.Hist Man page
VS.KS Man page
VS.QQ Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.