compareLists {OrderedList}R Documentation

Compare Ordered Lists with Weighted Overlap Score

Description

The two orderings recieved as parameters are compared using the weighted overlap score and compared with a random distribution of that score (yielding an empirical p-value).

Usage

compareLists(ID.List1, ID.List2, mapping = NULL, two.sided=TRUE, B = 1000, alphas = NULL, min.weight = 1e-5)

Arguments

ID.List1 first ordered list of identifiers to be compared.
ID.List2 second ordered list to be compared, must have the same length as ID.List1.
mapping maps identifiers between the two lists. This is a matrix with two columns. All items in ID.List1 must match to exactly one entry of column 1 of the mapping, each element in ID.List2 must match exactly one element in column 2 of the mapping. If mapping is NULL, the two lists are expected to contain the same identifiers and there must be a one-to-one relationship between the two.
two.sided whether the score is to be computed considering both ends of the list, or just the top members.
B the number of permutations used to estimate empirical p-values.
alphas a set of alpha candidates to be evaluated. If set to NULL, alphas are determined such that reasonable maximal ranks to be considered result.
min.weight the minimal weight to be considered.

Details

The two lists received as arguments are matched against each other according to the given mapping. The comparison is performed from both ends by default. Permutations of lists are used to generate random scores and compute empirical p-values. The evaluation is also performed for the case the lists should be reversed. From the resulting output, the set of overlapping list identifiers can be extracted using function getOverlap.

Value

An object of class listComparison is returned. It contains the following list elements:

n the length of the lists
call the input parameters
nn the maximal number of genes corresponding to the alphas and the minimal weight
scores scores for the straight list comparisons
revScores scores for the reversed list comparison
pvalues p-values for the straight list comparison
revPvalues p-values for the reversed list comparison
overlap number of overlapping identifiers per rank in straight comparison
revOverlap number of overlapping identifiers per rank in reversed comparison
randomScores random scores per weighting parameter
ID.List1 same as input ID.List1
ID.List2 same as input ID.List2


There are print and plot methods for listComparison objects. The plot method takes a parameter which to specify whether "overlap" or "density" is to be drawn.

Author(s)

Claudio Lottaz, Stefanie Scheid

References

Yang X, Bentink S, Scheid S, and Spang R (2006): Similarities of ordered gene lists, to appear in Journal of Bioinformatics and Computational Biology.

See Also

OrderedList, getOverlap

Examples

### Compare two artificial lists with some overlap
data(OL.data)
list1 <- as.character(OL.data$map$prostate)
list2 <- c(sample(list1[1:500]),sample(list1[501:1000]))
x <- compareLists(list1,list2)
x
getOverlap(x)

[Package OrderedList version 1.4.0 Index]