Description Usage Arguments Details Value Author(s) References Examples

Test whether the leading members of ordered lists significantly overlap.

1 | ```
cumOverlap(ol1, ol2)
``` |

`ol1` |
vector containing first ordered list. Duplicate values not allowed. |

`ol2` |
vector containing second ordered list. Should contain the same values as found in |

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 p-value.

The p-values are adjusted for multiple testing in a similar way to Bonferroni's method, but starting from the top of th e ranked list instead of from the smallest p-values. This approach is designed to be sensitive to contexts where the number of Ids involved in the significant overlap are a small proportion of the total.

The vectors `ol1`

and `ol2`

do not need to be of the same length, but only values in common between the two vectors will be used in the calculation.

This method was described in Chapter 4 of Wu (2011).

List containing the following components:

`n.total` |
integer, total number of values in common between |

`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

1 2 3 4 5 6 | ```
GeneIds <- paste0("Gene",1:50)
ol1 <- GeneIds
ol2 <- c(sample(GeneIds[1:5]), sample(GeneIds[6:50]))
coa <- cumOverlap(ol1, ol2)
coa$p.min
coa$id.overlap
``` |

```
[1] 2.359871e-06
[1] "Gene1" "Gene2" "Gene3" "Gene4" "Gene5"
```

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