HWE {GeneticsBase} | R Documentation |
Test the significances of Hardy-Weinberg Equilibrium (dis)equilibrium) statistics for each marker in a data set.
HWE(object, test = c("exact", "permutation", "chisq"), B = 10000, R = 1000, correct = TRUE, conf = c(0.95), na.rm = TRUE, founderOnly = TRUE, ...)
object |
a geneSet object. |
test |
specifys the test method. Available methods are “exact”, “permutation”, “chisq”. |
B |
an integer specifying the number of replicates used in the Monte Carlo test. Defaults to 10000. |
R |
Number of bootstrap iterations to use when computing the confidence interval. Defaults to 1000. |
correct |
see diseq.ci . |
conf |
Confidence level to use when computing the confidence level for linkage disequilibrium measures. Defaults to 0.95, should be in (0,1). |
na.rm |
logical. Should missing values be removed? |
founderOnly |
Indicates if only founders are used to do the test. |
... |
othere arguments used by the function chisq.test .
|
The function HWE
returns a list:
“diseq” |
a character string. |
call |
the matched call. |
“D” |
a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument conf . The first column is the estimated “D”. The next $p$ columns are estimated confidence limits for the confidence levels specified in the argument conf . The last two columns are the sample size and the p-value of the test that “D” is equal to zero. |
“D'” |
a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument conf . The first column is the estimated “D'”. The next $p$ columns are estimated confidence limits for the confidence levels specified in the argument conf . The last two columns are the sample size and the p-value of the test that “D'” is equal to zero. |
“r” |
a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument conf . The first column is the estimated “r”. The next $p$ columns are estimated confidence limits for the confidence levels specified in the argument conf . The last two columns are the sample size and the p-value of the test that “r” is equal to zero. |
“X$^2$” |
a matrix with $m$ rows and $3+p$ columns, where $m$ is the number of markers in the geneSet, $p$ is the number of elements of the argument conf . The first column is the test statistic “X$^2$” for HWE test. The next $p$ columns are zeros. The last two columns are the sample size and the p-value of the test for Hardy-Weinberg equilibrium. |
Gregory R. Warnes gregory.r.warnes@pfizer.com and Nitin Jain nitin.jain@pfizer.com
library(GeneticsBase) data(CAMP) HWE(CAMP)