Question: how to caculate enrichment score
0
gravatar for RC
3.3 years ago by
RC0
RC0 wrote:

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
fisher R • 1.9k views
ADD COMMENTlink written 3.3 years ago by RC0

odds ratio gives you the enrichment.

res <- fisher.test(x)
odds <- res$estimate
conf.int <- res$conf.int
ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Nicolas Rosewick8.7k

Thanks for your reply. But my OR is 0.92 (95%CI: 0.886-0.958) differs from the enrichment score in paper: enrichment score=1.09 (1.04 -1.13). I used the same input with the research, and our p values are consistent. Do i miss any steps?

ADD REPLYlink written 3.3 years ago by RC0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1063 users visited in the last hour