cumOverlap: Cumulative Overlap Analysis of Ordered Lists

In limma: Linear Models for Microarray Data

Description

Test whether the leading members of ordered lists significantly overlap.

Usage

cumOverlap(ol1, ol2)

Arguments

ol1	vector containing first ordered list. Duplicate values not allowed.
ol2	vector containing second ordered list. Should contain the same values as found in ol1 but in a possibly different order. Duplicate values not allowed.

Details

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).

Value

List containing the following components:

n.total	integer, total number of values in common between ol1 and ol2.
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 n.min.
id.overlap	vector giving the overlapping IDs in first n.min.
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.

Author(s)

Gordon Smyth and Di Wu

References

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

Examples

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

Example output

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

limma documentation built on Nov. 8, 2020, 8:28 p.m.