Question

Add up RLEs that are in lists?

1

Entering edit mode

gen ▴ 30

@gen-7383

Last seen 9.6 years ago

United States

Hi, I previously asked about summing RLEs but I'm now curious about extending the concept to summing lists of RLEs of arbitrary lengths. It seems fairly simple but I haven't seen a way to do it outside of loops.

Given something like...

$uc001aaa.3
numeric-Rle of length 249250621 with 5 runs
  Lengths:     14101        25       219        30 249236246
  Values :         0         1         0         1         0

$uc001aac.4
numeric-Rle of length 249250621 with 124 runs
  Lengths:             14345                30 ...                25         249221232
  Values :                 0 0.909090909090909 ... 0.909090909090909                 0

$uc001aae.4
numeric-Rle of length 249250621 with 29 runs
  Lengths:     14345        30      1163        13 ...       489        25 249231381
  Values :         0         1         0         1 ...         0         1         0

I know you can sum RLEs through result<-c(RLE1,RLE2) ie

integer-Rle of length 249250621 with 69798 runs
  Lengths:  20000646        25      2330        25 ...      2121        25 199255312
  Values :         0         1         0         1 ...         0         1         0

integer-Rle of length 249250621 with 69798 runs
  Lengths:  20000646        25      2330        25 ...      2121        25 199255312
  Values :         0         1         0         1 ...         0         1         0

=

integer-Rle of length 249250621 with 69798 runs
  Lengths:  20000646        25      2330        25 ...      2121        25 199255312
  Values :         0         2         0         2 ...         0         2         0

but I need to do it automatically with an arbitrary length list. Somehow being in a list form seems to prevent operations that would normally work.

reduce('+',RLElist)

sum(RLElist)

don't work, and I can't even sum elements of the list as I could RLEs that are not in a list.

thanks

RLE GenomicFeatures rnaseq • 2.2k views

ADD COMMENT • link updated 9.6 years ago by Hervé Pagès 16k • written 9.6 years ago by gen ▴ 30

score 1 · Answer 1 · 2015-04-10

Hi,

An important hint: if you know how to do it on an ordinary numeric vector, or list of numeric vectors, then you know how to do it on an Rle or RleList.

So le'ts first try to do this on a list of integer vectors:

x <- list(11:15,1:-3)
Reduce('+', x)
# [1] 12 12 12 12 12

Works! (Note that I used Reduce(), not reduce().)

Now on an RleList:

Reduce('+', RleList(x))
# integer-Rle of length 5 with 1 run
#   Lengths:  5
#   Values : 12

Also works!

In other words, there is nothing special about using Rles vs using ordinary numeric vectors or lists as long as basic arithmetic is concerned.

H.

score 0 · Answer 2 · 2015-04-10

0

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Ryan C. Thompson ★ 7.9k

@ryan-c-thompson-5618

Last seen 27 days ago

Icahn School of Medicine at Mount Sinai…

If you just want to take the sum of all the RLEs at once, you can do sum(sapply(RLEList, sum)). If you really want to combine them all into one big RLE, you can do that with unlist(RleList(x)). For summing, I would guess that the former is faster and more memory-efficient because it does not need to construct the full concatenation of all the RLEs.

ADD COMMENT • link 9.6 years ago Ryan C. Thompson ★ 7.9k

0

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Hi, yeah I want to get a big RLE not a single value. the second option unfortunately seems to give integer overflow errors.

rror in unlist(RleList(ExampleRLElist)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "S4Vectors") : 
  integer overflow while summing elements in 'lengths'

What do you think could be a solution? maybe something like runmean?

ADD REPLY • link 9.6 years ago gen ▴ 30

1

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Integer overflow means you will need to convert to numeric (i.e. floating point) because your sum is larger than the maximum representable integer. Note that you might lose some precision in the result.

ADD REPLY • link 9.6 years ago Ryan C. Thompson ★ 7.9k

0

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Hi, somewhat of a tangent, but if you wanted to shift a numeric RLE unchanged to a certain position or by a certain amount how could you do it?

The closest I can find is shiftApply which I believe lines two RLEs together? But it doesn't seem to work on an RLE in isolation.

ADD REPLY • link 9.6 years ago gen ▴ 30

0

Entering edit mode

Please ask this as a new question. Also make sure to explain what you mean by shifting a numeric Rle. What does it mean for example to shift an ordinary numeric vector? Do you mean padding with zeroes? Again, if you know how to do it on an ordinary numeric vector, then you know how to do it on a numeric Rle. For example, padding with 100 zeroes on the left:

x <- Rle(c(-0.4, 3), 14:15)
c(Rle(0, 100), x)
# numeric-Rle of length 19 with 3 runs
#   Lengths:  100   14   15
#   Values :    0 -0.4    3

H.

ADD REPLY • link 9.6 years ago Hervé Pagès 16k

0

Entering edit mode

The length of an Rle object cannot exceed 2^31-1. Unlisting your RleList object would result in an Rle object that exceeds that limit, hence the error. (The error message doesn't help, we should improve it.) Note that this limit is not just for Rle objects but for any vector-like or list-like object that derives from the Vector or List class (e.g. Hits, CharacterList, GRanges, GRangesList, GAlignments, etc...)

H.

ADD REPLY • link 9.6 years ago Hervé Pagès 16k