getOverlap {OrderedList} | R Documentation |
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.
getOverlap(x, max.rank = 100, percent = 0.95)
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 . |
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.
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
"density" is to be drawn.
Claudio Lottaz, Stefanie Scheid
Yang X, Bentink S, Scheid S, and Spang R (2006): Similarities of ordered gene lists, to appear in Journal of Bioinformatics and Computational Biology.
### 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)