WebSep 11, 2024 · $\begingroup$ @FrankHarrell, I forgot to mention that I am working in the rare setting (MAF < 0.1%), with thousands of hypotheses (i.e. 2x2 tables) so it is quite likely I will get expected cell counts exactly zero. It is also my experience from simulations that the $\chi^2$ statistic is too liberal and does not always control the FDR (i.e. inflation). WebDec 4, 2011 · Almost correct. If you look at ?phyper: phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) x, q vector of quantiles representing the number of white balls drawn …
Statistics for Bioinformatics - Practicals - Gene enrichment statistics
WebAug 1, 2024 · Computations in R, where dhyper and phyper are a PDF and a CDF of a hypergeometric distribution. Binomial approximation: Here Y ∼ B i n o m ( n = 500, p = .02). Then P ( Y = 10) = 0.1264 and P ( Y ≤ 10) = 0.5830. In these examples the binomial approximations are very good. WebYou are close, with your use of dhyper and phyper, but I don't understand where 0:2 and -1:2 are coming from. The p-value you want is the probability of getting 100 or more white balls in a sample of size 400 from an urn with 3000 white balls and 12000 black balls. Here are four ways to calculate it. dhb summer headband
Hypergeometric function - RDocumentation
Webwhich confirms the earlier calculations. If you want to test a number overlap, then the probability of getting that number or smaller from this model is. phyper (overlap, sampleb, totala - sampleb, samplec) and of getting that number or larger is. 1 - phyper (overlap - 1, sampleb, totala - sampleb, samplec) Share. Cite. Webdhyper gives the density, phyper gives the distribution function, qhyper gives the quantile function, and rhyper generates random deviates. Invalid arguments will result in return … WebFeb 21, 2011 · This is a little digression from Chapter 5 of Using R for Introductory Statistics that led me to the hypergeometric distribution. Question 5.13 A sample of 100 people is drawn from a population of … dhbw online bib stuttgart