Hi there, i am processing a genome-wide methylation data, and i wanna to find out which chromosome were enriched with differentially methylated probes(dmp). I noticed a research compared the distribution of dmps located on each chromosome.
for example, 8.87% of CpG probes on Chromosome 13 were identified as Bonferroni-significant dDMPs (relative enrichment = 1.26, P = 3.68 × 10−10), whereas only 4.09% of CpG probes on Chromosome 19 reach this criterion (relative enrichment = 0.55, P = 7.01 × 10−79).
(reference: Spiers H, Hannon E, Schalkwyk LC, et al. Methylomic trajectories across human fetal brain development. Genome Research. 2015;25(3):338-352. doi:10.1101/gr.180273.114.)
The METHOD part mentioned that the enrichment analysis was done by fisher's exact test, so i try to use fisher.test in R to replicate the result. However, i get a same P value but i have no idea how to caculate the enrichment score. The imput data as following:
Chromosome TotalProbes SignificantProbes (%) Enrichment(95% CI) p value 1 40079 3109 (7.76) 1.09 (1.04 -1.13) 3.56E-05 Total 399364 28718 (7.19) NA NA
The METHOD part mentioned that the enrichment analysis was done by fisher's exact test, so i try to use fisher.test in R to replicate the result. However, i get a same P value but i have no clue how to caculate the enrichment score. Any idea? Any suggestion will be appreciated!
> x<-c(40079-3109,3109,399364-28718,28718) > dim(x)<-c(2,2) > fisher.test(x) Fisher's Exact Test for Count Data data: x p-value = 3.558e-05 alternative hypothesis: true odds ratio is not equal to 1 95 percent confidence interval: 0.8864884 0.9578336 sample estimates: odds ratio 0.9213249