Let me first state my problem. I am analyzing a genome and its genes. I can calculate proportions of different types of genes in the genome (pseudogenes, lincRNAs, coding_genes...). Now, I have particular genomic regions of interest and the corresponding list of genes belonging to these regions. I want to test if genes of type X (e.g. pseudogenes) have the same frequency in this region as in the whole genome.
I have been playing with different tests. Firstly, the binom.test, assuming that p=freq_in_genome, n=number of genes in the regions of interest and x=number of successes (number of genes of type X). However, I am not sure if this is the most appropriate test and have been looking for alternatives to test for equal proportions: fisher's exact test, on one-sample z-test, prop.test in R, etc... (some of them are probably the same ¿?)