In HWxtest: Exact Tests for Hardy-Weinberg Proportions
Description Usage Arguments Value References Examples
Description
The hwx.test()
function is the main function of the HWxtest
package. This function produces a valid test for Hardy-Weinberg frequencies for virtually any set of genotype counts. It will use either a full-enumeration method in which all possible tables with the same allele numbers are examined, or a Monte Carlo test where a large number of random tables is examined. To decide which to use, it calls xcountCutoff
to determine whether the number of tables to examine is greater than cutoff
. If it is, then mtest
is used. Otherwise xtest
is used. The result is a robust test which will always provide a meaningful and accurate P value. Each table examined is compared with the observed counts according to each of four measures of fit: “LLR”, “Prob”, “U”, or “Chisq” corresponding to the log-likelihood ratio, the null-hypothesis probability, the U-score or the Pearson X^2 value. It can also plot a histogram showing the distribution of any of these statistics.
Usage
123 | hwx.test(c, method = "auto", cutoff = 1e+07, B = 1e+05, statName = "LLR", histobins = 0, histobounds = c(0, 0), showCurve = T, safeSecs = 100, detail = 2) |
Arguments
c | The genotype counts. You must provide the number of each genotype. So if there are k alleles, you need to include the number of each of the k(k+1)/2 genotypes. The format of |
method | Can be “auto”, “exact” or “monte” to indicate the method to use. If “auto”, the |
cutoff | If |
B | The number of trials to perform if Monte Carlo method is used |
statName | can be “LLR”, “Prob”, “U”, or “Chisq” depending on which one is to be ploted. Note that P values for all four are computed regardless of which one is specified with this parameter. |
histobins | If 0, no histogram is plotted. If 1 or |
histobounds | A vector containing the left and right boundaries for the histogram's x axis. If you leave this as the default, |
showCurve | whether to show a blue curve indicating the asymptotic (chi squared) distribution. This only works for |
safeSecs | After this many seconds the calculation will be aborted. This is a safety valve to prevent attempts to compute impossibly large sets of tables. |
detail | Determines how much detail is printed. If it is set to 0, nothing is printed (useful if you use |
Value
Returns a list of class hwtest
which includes the following items:
$ Pvalues | The four computed P values corresponding to the test statistics: |
$ observed | The four observed statistics in the same order as above |
$ ntrials | The number of tables examined during the calculation if done by Monte Carlo |
$ tableCount | The total number of tables if done by full enumeration |
$ genotypes | The input matrix of genotype counts |
$ alleles | The allele counts m corresponding to the input genotype counts |
$ statName | Which statistic to use for the histogram and in the |
$ method | Which method was used, “exact” or “monte” |
$ detail | An integer indicating how much detail to print. Use 0 for no printing |
$ SE | vector with the standard error for each stat. Only applicable with Monte Carlo tests |
References
The methods are described by Engels, 2009. Genetics 183:1431.
Examples
1234567 | # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:c <- c(0,3,1,5,18,1,3,7,5,2)hwx.test(c)# To see a histogram of the LLR statistic:hwx.test(c, histobins=TRUE)# For a histogram of the U statistic and other details of the result:hwx.test(c, statName="U", histobins=TRUE, detail=3) |
HWxtest documentation built on May 31, 2019, 9:04 a.m.
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