| cumOverlap {limma} | R Documentation |
Test whether the leading members of ordered lists significantly overlap.
cumOverlap(ol1, ol2)
ol1 |
vector containing first ordered list. |
ol2 |
vector containing second ordered list. |
The function compares the top n members of each list, for every possible n, and conducts an hypergeometric test for overlap.
The function returns the value of n giving the smallest Bonferroni adjusted p-value.
This method was described in Chapter 4 of Wu (2011).
List containing the following components:
n.min |
integer, top table length leading to smallest adjusted p-value. |
p.min |
smallest adjusted p-value. |
n.overlap |
integer, number of overlapping IDs in first |
id.overlap |
vector giving the overlapping IDs in first |
p.value |
numeric, vector of p-values for each possible top table length. |
adj.p.value |
numeric, vector of Bonferroni adjusted p-values for each possible top table length. |
Gordon Smyth and Di Wu
Wu, D (2011). Finding hidden relationships between gene expression profiles with application to breast cancer biology. PhD thesis, University of Melbourne. http://hdl.handle.net/11343/36278
ol1 <- letters[1:26] ol2 <- letters[sample(26)] coa <- cumOverlap(ol1, ol2) coa$p.min