I'm working on DNA sequencing data, and have 8 samples from a single cohort, all samples having undergone the same mutagenic treatment (one group, no independent variable). Six mutation classes (Mut1-Mut6) are found in the samples with varying frequencies/counts. As is quite apparent from the data shown below, Mut4 occurs at a higher frequency than the other mutation classes:
Mut1 Mut2 Mut3 Mut4 Mut5 Mut6 Sample1 88 27 26 508 51 40 Sample2 438 108 102 1828 184 145 Sample3 334 78 92 1454 151 131 Sample4 146 38 41 448 40 24 Sample5 165 39 54 420 43 37 Sample6 79 20 28 244 39 20 Sample7 133 30 40 404 35 29 Sample8 119 37 54 382 44 40
I would like to show that across the entire cohort, Mut4 occurs at a higher frequency than the other mutations classes, but can't figure out an appropriate way to do this.
To me, this seems like a chi-squared test would be the most appropriate, with a null hypothesis of a flat distribution. Using R, and having read the data in as
freq, this can quite easily be tested for a single sample using the
chisq.test(freq[1,], p=rep(1/6, times=6))
However, I would like to test this across the whole cohort, not just the single sample. I've considered summing all the mutation counts across the cohort, but this would lead to issues with certain samples being weighted more than others (f.ex. sample 2 and 3 have very high mutation counts compared to sample 6). This issue could be mitigated by using proportions instead of count, but I'm unsure if this is a proper way to perform this test.
I've also tried running the chisq.test command on the entire dataset as follows:
chisq.test(freq, p=rep(1/6, times=6))
But I'm unsure of how the results are actually calculated, and am thrown off by the fact that the results seem to be completely unaffected by what I enter as the values for
Am I on the right track using a chi-squared, and if so, what is the correct way to move forward from here? Or am I completely off track, and if so, what would be the correct way to test if Mut4 occurs more frequently than the other mutation classes?