Question

IRanges start bigger than end

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vedran.franke • 0

@vedranfranke-7218

Last seen 6.8 years ago

Germany

I was just wondering why this code doesn't produce an error?

IRanges(start=1,end=0)

Best regards,

Vedran

I'm using IRanges_2.2.9

iranges • 1.2k views

ADD COMMENT • link 8.9 years ago vedran.franke • 0

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Why do you think it should produce an error? The starting position of a range has nothing to do with the width.

ADD REPLY • link 8.9 years ago James W. MacDonald 67k

score 2 · Accepted Answer · 2016-02-18

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.1 years ago

United States

I think you mean why can the start be larger than the end? If the start is 1 less than the end, it indicates an empty range.

ADD COMMENT • link 8.9 years ago Michael Lawrence ★ 11k

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Thank you for the prompt answer!

I edited the question for the clarification - width was a typo.

Could you please just clarify the logic behind this implementation?

I still do not see why the above creates a valid IRanges object?

ADD REPLY • link 8.9 years ago vedran.franke • 0

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Hi,

Zero-width ranges are used to represent insertion points. It might be a little bit shocking at first to see a start that is equal to end + 1 but that's because we use a representation where the interval is closed on both sides:

IRanges(11, width=3:0)
# IRanges of length 4
#     start end width
# [1]    11  13     3
# [2]    11  12     2
# [3]    11  11     1
# [4]    11  10     0

The last range is a zero-width range. It represents an insertion between positions 10 and 11. Yes it might be a little bit shocking to see that it ends before it even started but... what else could the start and end be for this range?

For example such zero-width range can be used to perform an insertion in a DNA sequence:

library(Biostrings)
## Insert 3 nucleotides between positions 10 and 11:
replaceAt(DNAString("AAAAATTTTTGG"), IRanges(11, 10), "ACA")
##   15-letter "DNAString" instance
## seq: AAAAATTTTTACAGG

Hope this helps,

H.

ADD REPLY • link 8.9 years ago Hervé Pagès 16k

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The problem arose when a student used a combination of trim(shift()) on a GRanges object, and

obtained a range with coordinates of start=1 and end=0.

This makes sense now.

Thank you so much!

ADD REPLY • link 8.9 years ago vedran.franke • 0