Description Usage Arguments Details Value Author(s) References See Also Examples
A Monte Carlo permutation method for multiple OR(odd ratio) test correction in case/control association study.
1 | OR.MCPerm(case_allele1, case_allele2, control_allele1, control_allele2, repeatNum = 1000)
|
case_allele1 |
a non-negative integer, the frequency of allele1 in case samples. |
case_allele2 |
a non-negative integer, the frequency of allele2 in case samples. |
control_allele1 |
a non-negative integer, the frequency of allele1 in control samples. |
control_allele2 |
a non-negative integer, the frequency of allele2 in control samples. |
repeatNum |
an integer(default 1000) specifying the number of replicates used in the Monte Carlo permutation. |
The odds ratio is a measure of effect size, describing the strength of association or non-independence between two binary data values.
"OR.MCPerm" simulates permutation method to get p value for risk_allele, by generating random numbers
for the hypergeometric distribution based on the genotype statistic of original data. Seealso chisq.MCPerm
.
risk_allele |
risk_allele. |
pValue |
the p value for the test. |
obsOR |
the OR value for the true data. |
permOR |
a vector with 'repeatNum' elements, the OR value for the simulation data. |
Lanying Zhang and Yongshuai Jiang <jiangyongshuai@gmail.com>
William S Noble(Nat Biotechnol.2009): How does multiple testing correction work?
Edwards, A.W.F.(1963): The measure of association in a 2x2 table.
Edgington. E.S.(1995): Randomization tests, 3rd ed.
OR
,
OR.TradPerm
,
Armitage
,
Armitage.TradPerm
,
Armitage.MCPerm
,
chisq.test
,
chisq.TradPerm
,
chisq.MCPerm
,
fisher.test
,
fisher.TradPerm
,
fisher.MCPerm
,
meta
,
meta.TradPerm
,
meta.MCPerm
,
permuteGenotype
,
rhyper
,
permuteGenotypeCount
,
genotypeStat
1 2 3 4 5 | # case_allele1=23
# case_allele2=34
# control_allele1=26
# control_allele2=29
# OR.MCPerm(23,34,26,29,repeatNum=100000)
|
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