orthoverlap.test: Orthogroup test for over- or underrepresentation

In msaul/msaul: Michael C. Saul's Personal R Package

Description

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.

Usage

orthoverlap.test(list1.s1, list2.s2, orthodb.index.s1, orthodb.index.s2,
  B = 30000, representation = "over", save.distribution = FALSE)

Arguments

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)

Author(s)

Michael C. Saul

msaul/msaul documentation built on May 23, 2019, 7:50 a.m.