0
$\begingroup$

I have mutational catalogues of 4 samples like below

> head(out)
        Responders1 Nonresponders1 Responders2 Nonresponders2
A[C>A]A       11744          13546        2897           3655
A[C>A]C        5144           7172        2295           2163
A[C>A]G         939           1257         290            279
A[C>A]T        6065           7997        2078           2088
C[C>A]A        8969          11155        2055           2582
C[C>A]C        4050           6657        1367           1173
>

 > dim(mut)
[1] 96  4
> 

Note: A[C>A]A - Single nucleotide base substitution

I want to look if mutational substitutions are different between samples

I have tried

wilcox.test(mut$Responders2,mut$Nonresponders2)

t.test(mut$Responders2,mut$Nonresponders2)

var.test(mut$Responders2,mut$Nonresponders2)
fisher.test(mut$Responders2,mut$Nonresponders2,simulate.p.value=TRUE)

kruskal.test(mut$Responders2,mut$Nonresponders2)

To find a difference but I think you may know a better test to find any difference here

This is base shift (mutation, substitution across genome of each patient). I guess mutations happen randomly but I don't know if mutational caller algorithm also pick them by randomness. I expect the shift of A (Adenine) to C (Cytosine) in a group of these patients be higher than the other group. This higher rate likely should be due to some background than randomness picked by algorithm. So I think null hypothesis is that rate of base shifting is not the same in both group. I also don't expect a normalised distribution of base shifting rather a poison distribution.

Can you help please?

Thanks

$\endgroup$
0
0
$\begingroup$

Answer from @fabio-marroni, converted from comment:

You might try to use mutationalPatterns and see if the responders cluster together and separated from nonresponders.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.