segmentPrune | R Documentation |
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 |
verb |
integer level of verbosity, 0: no messages, 1: show messages. |
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