OrderedList (version 1.44.0)

getOverlap: Extracting the Intersecting IDs From a listComparison Object

Description

This function extracts the intersecting set of list identifiers from an object of class listComparison as output of function compareLists. The user has to specify the maximum rank to be considered to receive the intersecting set up to this rank.

Usage

getOverlap(x, max.rank = NULL, percent = 0.95)
"plot"(x, which="overlap", no.title=FALSE,  no.legend=FALSE, list.name1="List 1", list.name2="List 2", ...)

Arguments

x

An object of class listComparison.

max.rank

The maximum rank to be considered.

percent

The final list of overlapping genes consists of those probes that contribute a certain percentage to the overall similarity score. Default is percent=0.95. To get the full list of genes, set percent=1.

which

select what to draw, either 'overlap' or'scores'.

no.title

whether to generate a title automatically.

no.legend

whether to generate a legend automatically.

list.name1

A name for the first list provided to compareLists.

list.name2

A name for the second list provided to compareLists.

...

Further arguments passed on to generic plot.

Value

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

n

the length of the lists.

call

the parameters of the input object.

nn

the input max.rank.

score

the observed similarity score.

pvalue

p-values for the observed score.

overlaps

number of overlapping identifiers per rank.

randomScores

random scores for given parameters.

direction

numerical value. Returns '1' if the similarity score is higher for the originally ordered lists and '-1' if the score is higher for the comparison of one original to one reversed list.

intersect

Vector with the sorted overlapping list identifiers, which contribute percent to the overall similarity score.

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

Details

Function compareLists returns a list comparison for several choices of alpha. The number of genes to be taken into account differs dependent on alpha. One might now want to fix the number of genes and receive the resulting set of intersecting list identifiers. To this end, the user chooses a maximum rank to be considered from the values in column 'Genes' of the listComparison object. The direction (original or reversed) will internally be set to the direction yielding the higher similarity score.

If two.sided was TRUE, the first max.rank IDs on top of the lists and the first max.rank identifiers at the end of the lists are considered. If two.sided was FALSE, only the max.rank top identifiers are evaluated for overlap.

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, compareLists

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)