Question: AF comparison between two population.
0
gravatar for always_learning
12 months ago by
Doha, Qatar
always_learning980 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?

af r statistical test • 338 views
ADD COMMENTlink written 12 months ago by always_learning980
1

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

ADD REPLYlink written 12 months ago by ATpoint23k

What is not clear in my Question?

ADD REPLYlink written 12 months ago by always_learning980

Please provide example data.

ADD REPLYlink written 12 months ago by WouterDeCoster40k

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

ADD REPLYlink written 12 months ago by always_learning980

Please find dropbox link for example data.

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

ADD REPLYlink written 12 months ago by always_learning980

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

ADD REPLYlink written 12 months ago by Kevin Blighe48k

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

ADD REPLYlink written 12 months ago by always_learning980
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