Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/Armitage.MCPerm.R
A Monte Carlo permutation method for Armitage's trend test in case/control association study.
1 2 | Armitage.MCPerm(case_11, case_12, case_22, control_11, control_12, control_22,
repeatNum = 1000)
|
case_11 |
a non-negative integer, the frequency of genotype "allele1/allele1" in case samples. |
case_12 |
a non-negative integer, the frequency of genotype "allele1/allele2" in case samples. |
case_22 |
a non-negative integer, the frequency of genotype "allele2/allele2" in case samples. |
control_11 |
a non-negative integer, the frequency of genotype "allele1/allele1" in control samples. |
control_12 |
a non-negative integer, the frequency of genotype "allele1/allele2" in control samples. |
control_22 |
a non-negative integer, the frequency of genotype "allele2/allele2" in control samples |
repeatNum |
an integer(default 1000) specifying the number of replicates used in the Monte Carlo permutation. |
The Cochran-Armitage test for trend, is used in categorical data analysis when the aim is to assess for the presence of an association between a variable with two categories and a variable with k categories. It modifies the Pearson chi-squared test to incorporate a suspected ordering in the effects of the k categories of the second variable. The trend test is ofen used as a genotype-based test for case/control genetic association studies.
"Armitage.MCPerm" simulates permutation method to correct p value, by twice generating random numbers for the
hypergeometric distribution based on the genotype statistic of original data. Seealso chisq.MCPerm
.
pValue |
the p value for the test. |
obsStatistic |
the statistic of Armitage's trend test for the true data. |
obsP |
the p value for Armitage's trend test of the true data. |
permStatistic |
a vector with 'repeatNum' elements, the statistic of Armitage's trend test for the simulation data. |
permP |
a vector with 'repeatNum' elements, the p value for Armitage's trend test for the simulation data. |
Lanying Zhang and Yongshuai Jiang <jiangyongshuai@gmail.com>
William S Noble(Nat Biotechnol.2009): How does multiple testing correction work?
statgen.org(2007): A derivation for Armitage's trend test for the 2x3 genotype table.
OR
,
OR.TradPerm
,
OR.MCPerm
,
Armitage
,
Armitage.TradPerm
,
chisq.test
,
chisq.TradPerm
,
chisq.MCPerm
,
fisher.test
,
fisher.TradPerm
,
fisher.MCPerm
,
meta
,
meta.TradPerm
,
meta.MCPerm
,
permuteGenotype
,
rhyper
,
permuteGenotypeCount
,
genotypeStat
1 2 | ## Armitage.MCPerm(case_11=4,case_12=1,case_22=1,control_11=3,
# control_12=5,control_22=7,repeatNum=10000)
|
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