View source: R/adapted.cmh.test.true.R
adapted.cmh.test.true | R Documentation |
This function performs the adapted CMH test (Spitzer et al. 2019), but in cases where all frequencies are known, and the only variance of data comes from genetic drift. Drift variance is the only variance included in this test.
adapted.cmh.test.true(freq, Ne, gen, repli)
freq |
Numeric matrix of frequencies, with the row being the haplotype/SNP, and column being the sequenced time points. |
Ne |
Numeric vector with length as number of replicates, containing information of Ne (effective population size) at each replicated population. If Ne changes over time, take as input a numeric matrix, with the column being the replicate position, row being the Ne at each sequenced time points. |
gen |
Numeric vector of sequenced time points. |
repli |
Numeric, specifying the number of replicated populations. |
Numeric vector, p-values from the hypothesis test
Spitzer, K., Pelizzola, M., Futschik, A., (2019), Modifying the Chi-square and the CMH test for population genetic inference: adapting to over-dispersion, The Annals of Applied Statistics 14(1): 202-220.
haplotest()
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