calcHypPI
(Package: matchBox) :
Probability intervals calculation for CAT curves using the hypergeometric distribution.
The calcHypPI function calculates probability intervals for a correspondence at the top (CAT) curve using the hypergeometric distribution. This function, based on the qhyper quantile function, produces a probability intervals matrix to be passed as argument to plotCat in order to add probability intervals shades when plotting CAT curves.
computeCat
(Package: matchBox) :
Computing overlap proportions among ordered vectors
computeCat computes the overlap proportions between pairs of ordered vectors of identifiers. The input to this function is a data.frame containing non-redundant identifiers and a number of ranking statistics organized by columns. This function enables comparing all possible pair combinations, or selecting one column as the reference ranking for the remaining. The output of this function can be used as the input to plotCat, which creates correspondence at the top curves, as used in Irizarry et al, Nat Methods (2005), for comparing differential gene expression across platforms and labs.
filterRedundant
(Package: matchBox) :
This functions removes redundant features from a data.frame
Prior computing proportion of overlap between ranked vector of features it is necessary to remove the redundant features. This can be accomplished using a number of methods implemeted in the filterRedundant function, as explained below.
The matchBox package allows to annotate and compare ranked vectors (e.g. by differential expression) of genomic features (e.g. genes, or probe sets), using CAT curves. A CAT curve displays the overlap proportion between two ranked vectors of identifiers against the number of considered features. This techiques was used for comparing differential gene expression results obtained from different platforms in different laboratories (see Irizarry et al, Nat Methods (2005))
mergeData
(Package: matchBox) :
Merging data.frames based on common identifiers
This utility function is used for merging specific columns from a set of distinct data.frames based on a specific set of identifiers. For instance this utility function can be used to retrieve from multiple data.frames the ranking statistics and the identifiers that will be used for computing the correspondence at the top curves.
plotCat
(Package: matchBox) :
Plotting correspondence at the top curves
This function plots corresponding at the top (CAT) curves using overlap proportions computed by computeCat. A number of arguments can be used for a pretty display, and for annotating the plot, and adding the legend
providing 
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