regionCAT: regionCAT

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

regionCAT

Description

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)

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).

Value

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

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)

ETHZ-INS/epiwraps documentation built on May 4, 2024, 6:25 a.m.