Description Usage Arguments Author(s)
For four character vectors (list1.s1, list2.s2, orthodb.index.s1, orthodb.index.s2), this function computes a randomization-based p-value of the overlap. It can test for either overrepresentation or underrepresention. Orthoverlap uses a normal approximation of the hypergeometric distribution to make scores from different distributions directly comparable. It calculates the p-value by comparing the Pearson correlation coefficient derived from data with orthology to a sample with orthology bootstrapped.
1 2 | orthoverlap.test(list1.s1, list2.s2, orthodb.index.s1, orthodb.index.s2,
B = 30000, representation = "over", save.distribution = FALSE)
|
list1.s1 |
the first test list from species 1 |
list2.s2 |
the second test list from species 2 |
orthodb.index.s1 |
a data frame indexing IDs from list 1 to OrthoDB IDs |
orthodb.index.s2 |
a data frame indexing IDs from list 2 to OrthoDB IDs |
B |
the number of randomizations to perform (defaults to 30000) |
representation |
test for overrepresentation or underrepresentation (defaults to "over") |
save.distribution |
write out distribution to output (defaults to FALSE) |
Michael C. Saul
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