regionCAT

Computes/plots the 'concordance at the top' (CAT) of two lists of genomic regions.

Usage

regionCAT(
  regions1,
  regions2,
  start = 5L,
  concord.type = c("both", "inTop", "inAll"),
  returnData = FALSE,
  ignore.strand = TRUE
)

Arguments

regions1, regions2

A GRanges object with a `score` metadata column according to which the regions will be ranked (descending).

start

The rank at which to start plotting (removes large variations at the beginning when very few regions are considered)

concord.type

Concordance type to plot, either 'inTop', 'inAll', or 'both' (see details). Ignored if `returnData=TRUE`.

returnData

Logical; whether to return the data instead of plotting.

ignore.strand

Logical; whether to ignore the strand for computing overlap (default TRUE)

Value

A ggplot object, or a data.frame if `returnData=TRUE`.

Details

The two concordance types are as follows: * 'inTop' indicates the proportion of the top X regions that are in the top X in both lists. * 'all' indicates the proportion of the top X regions that are anywhere in the other list (since this relationship is asymmetrical, the mean of both two directions is used).

Examples

# we create two GRanges with scores, which have similar high-score peaks but
# the rest random:
gr1 <- GRanges("seq1", IRanges(runif(20,1,2000), width=20),
               score=20:1)
gr2 <- GRanges("seq1", c(head(ranges(gr1),5),
                         IRanges(runif(15,1,2000), width=20)),
               score=c(20:16, sample.int(15)))
regionCAT(gr1,gr2)