Question: AF comparison between two population.

0

always_learning •

**1.0k**wrote:Hi,

I have Allele Frequenct frequency data for Population A and I wanted to compare this with Population B. Below is the script that I wrote for Chi Square test between AF for these two population.

```
library("dplyr")
input = fread("GENE_PANEL_MUTATION.tsv", sep = "\t") inputTtest = filter(input, !complete.cases(gnomadWGS_AF, new_AF))
inputTtest = input %>% select(gnomadWGS_AF,new_AF) %>%
filter(complete.cases("NA")) %>%
na.omit() %>%
filter(!is.na(as.numeric(gnomadWGS_AF)))
inputTtest$gnomadWGS_AF=as.numeric(inputTtest$gnomadWGS_AF) inputTtest$new_AF=as.numeric(inputTtest$new_AF)
chisq <- function(a,b){ data <- matrix(c(a,b),ncol=2) mode(data) = "numeric" print (data) c(p = chisq.test(data)$p.value,
OR = chisq.test(data)$estimate) }
inputTtest %>% rowwise() %>% mutate(p=chisq(gnomadWGS_AF,new_AF)[[1]])
```

I am not getting any significant P-value while I can see that I have SNP's where frequencies are significantly different between both populations. Can someone help me with this? Which test I should apply?

Please provide example data. You might be inspired by How to ask good questions in technical and scientifc forums.

36kWhat is not clear in my Question?

1.0k44kPlease find dropbox link for example file. https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0

1.0kPlease find dropbox link for example data.

https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0

1.0kDo the Chi Square test. While you're at it, calculate the OR, confidence intervals, and Z-score, too: A: SNP dataset and Z Score

63kThanks !! But I have just frequencies !! So I don't think that I can do similar to that.

1.0k