sortOverlaps: sorts cluster overlap structure by p-values

In raim/segmenTools: Tools for Functional Genome Exploration

sorts cluster overlap structure by p-values

Description

Sorts one dimension of a cluster overlap structure by their p-values along the sorting of the other axis. For each cluster along the pre-sorted (non-selected) axis, the most significant overlaps (p<p.min) are chosen and moved to the top of the matrix.

Usage

sortOverlaps(
  ovl,
  axis = 2,
  p.min = 0.05,
  cut = FALSE,
  srt,
  sign = 0,
  symmetric = "no"
)

Arguments

ovl	a ‘clusterOverlaps’ object returned by clusterCluster
axis	axis to sort (2 for y-axis/rows, 1 for x-axis/columns)
p.min	significance cutoff during sorting
cut	remove all overlaps without any p<p.min
srt	sorting vector for rows, if this is passed the significance sorting is skipped
sign	sort only by p-values of this sign (-1,+1) for two-sided tests.
symmetric	indicate whether the overlap matrix is symmetric with symmetric="upper" or symmetric="lower".

raim/segmenTools documentation built on Sept. 25, 2024, 5:38 p.m.