clean_granges_for_cesa | R Documentation |
Tries to format an input GRanges object to be compatible with a CESAnalysis reference genome. Optionally, also applies padding to start and end positions of ranges, stopping at chromosome ends. Either stops with an error or returns a clean granges object.
clean_granges_for_cesa(
cesa = NULL,
gr = NULL,
padding = 0,
refset_env = NULL,
reduce_sort_strip = TRUE
)
cesa |
CESAnalysis; required unless refset_env is supplied directly. |
gr |
GRanges object |
padding |
How many bases to expand start and end of each position |
refset_env |
A reference data set environment. Required if cesa is not specified. |
reduce_sort_strip |
Unstrands and calls reduce(gr) which also drops all metadata columns, and then sorts the final gr. Default TRUE; use FALSE to preserve original gr structure. |
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