Question: AF comparison between two population.
0
gravatar for always_learning
23 months ago by
always_learning1.0k
Doha, Qatar
always_learning1.0k 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?

af r statistical test • 503 views
ADD COMMENTlink written 23 months ago by always_learning1.0k
1

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

ADD REPLYlink written 23 months ago by ATpoint36k

What is not clear in my Question?

ADD REPLYlink written 23 months ago by always_learning1.0k

Please provide example data.

ADD REPLYlink written 23 months ago by WouterDeCoster44k

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

ADD REPLYlink written 23 months ago by always_learning1.0k

Please find dropbox link for example data.

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

ADD REPLYlink written 23 months ago by always_learning1.0k

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 23 months ago by Kevin Blighe63k

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

ADD REPLYlink written 23 months ago by always_learning1.0k
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