getVennCounts: getVennCounts

In amitjavilaventura/seqViewR: Visualization of Omics And Sequencing Data In R

getVennCounts

Description

Function that calls 'ChIPpeakAnno::makeVennDiagram()' to obtain the venn counts. It also does a list of peaks and with several variables corresponding to the presence of these peaks in each set. It's a helper for other functions to draw Venn diagrams or UpSet plots for peak intersections.

Usage

getVennCounts(
  peaks,
  conds = names(peaks),
  conds_order = conds,
  stranded = FALSE,
  plot = FALSE
)

Arguments

peaks	List of dataframes with the genomic coordinates of the regions to overlap. Dataframes must contain the columns seqnames, start, end.
conds	Character with the same length as the 'peaks' list. The names that are given to the diferente objects in the 'peaks' list. Default: 'names(peaks)'
conds_order	Character of the same length as 'conds'. Same values as in 'conds' but with the desired order of priority. Default: 'conds'.
stranded	Logical of length 1. If TRUE, it considers the strand information to do the overlaps. Default = FALSE.
plot	Logical of lenght 1. Whether to draw the the 'makeVennDiagram()' plot or not. Default: FALSE

Author(s)

amitjavilaventura

See Also

ChIPpeakAnno::makeVennDiagram

amitjavilaventura/seqViewR documentation built on Nov. 21, 2023, 10:12 a.m.