Hi,
I think there should be a trim = TRUE/FALSE option in the 'resize' function to avoid such warnings below. Since there is otherwise no straightforward way to resize without exceeding chromosome coordinate boundaries.
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 46 out-of-bound ranges located on sequences
chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11,
chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21,
chr22, and chrX. Note that ranges located on a sequence whose length is
unknown (NA) or on a circular sequence are not considered out-of-bound
(use seqlengths() and isCircular() to get the lengths and circularity
flags of the underlying sequences). You can use trim() to trim these
ranges. See ?trim,GenomicRanges-method for more information
Hi,
I think there should be a trim = TRUE/FALSE option in the 'resize' function to avoid such warnings below. Since there is otherwise no straightforward way to resize without exceeding chromosome coordinate boundaries.
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 46 out-of-bound ranges located on sequences
chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11,
chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21,
chr22, and chrX. Note that ranges located on a sequence whose length is
unknown (NA) or on a circular sequence are not considered out-of-bound
(use seqlengths() and isCircular() to get the lengths and circularity
flags of the underlying sequences). You can use trim() to trim these
ranges. See ?
trim,GenomicRanges-methodfor more information