segmentPrune: prune genomic coordinates at chromosome ends
In raim/segmenTools: Tools for Functional Genome Exploration

segmentPrune

R Documentation

prune genomic coordinates at chromosome ends

Cuts segments coordinates that are beyond chromosome coordinates.

segmentPrune(
  x,
  chrL,
  chr = "chr",
  coors = c(start = "start", end = "end", coor = "coor"),
  remove.empty = FALSE,
  verb = 1
)

`x`	genomic interval (segments) table.
`chrL`	chromosome length vector, where the chromosome column must provide the index in this vector; e.g. for 16 chromosomes, chrL has length 16 and provides, in this order, the lengths of chromosomes 1 to 16).
`chr`	chromosome column name.
`coors`	coordinate column names to cut.
`remove.empty`	after pruning, remove any segments with length 0; NOTE: that this also affects segments that were not pruned, and already had length 0 in `x`.
`verb`	integer level of verbosity, 0: no messages, 1: show messages.