summing integer RLE
1
0
Entering edit mode
gen ▴ 30
@gen-7383
Last seen 7.5 years ago
United States

Hi,

Say you have something like this RleListexample

RleList of length 4
$seq1 integer-Rle of length 1575 with 42 runs Lengths: 982 1 1 2 3 2 2 1 1 1 ... 1 1 1 2 1 1 3 1 531 Values : 0 2 3 6 8 10 12 13 15 17 ... 12 11 10 8 7 5 4 2 0$seq2
integer-Rle of length 1584 with 1 run
Lengths: 1584
Values :    0

$seq1 integer-Rle of length 1575 with 42 runs Lengths: 982 1 1 2 3 2 2 1 1 1 ... 1 1 1 2 1 1 3 1 531 Values : 0 2 3 6 8 10 12 13 15 17 ... 12 11 10 8 7 5 4 2 0$seq2
integer-Rle of length 1584 with 1 run
Lengths: 1584
Values :    0

How would you add or average the values of only the seq1 RLEs into one single RLE object?

When I try sum(RleListexample) it collapses everything into one number. When I try RleListexample\$seq1 it doesn't provide me with the two RLEs in the list it just provides me with one.

rle list irange grangeslist • 1.2k views
ADD COMMENT
1
Entering edit mode
Chris Seidel ▴ 80
@chris-seidel-5840
Last seen 16 months ago
United States

Your Rle object has the same name for more than one element. Since this doesn't provide specificity, if you want to sum a particular element, you might refer to it specifically (i.e. not by name):

sum(RleListexample[[1]])

Or if you want to sum all the elements named "seq1" you might create a boolean index:

sum(RleListexample[names(RleListexample) == "seq1"])

ADD COMMENT
0
Entering edit mode

Hi, thanks but the answer collapses the RLE into one number. I need to find the average RLE in an RLElist. IE for two sets of coverage data. Combine them into one set and then average it out for mean coverage.

thanks

ADD REPLY
1
Entering edit mode

Maybe you are looking for something like (RleListexample[1:2] + RleListexample[3:4]) / 2 ? As Chris suggested, it's probably more usual to think of averaging two separate objects

library(GenomicAlignments)
cvg1 = coverage(BamFile("first.bam"))
cvg2 = coverage(BamFile("second.bam"))
avecvg = (cvg1 + cvg2) / 2

ADD REPLY
0
Entering edit mode

cool it works for individual RLEs. I might need to do something with lists though.

ADD REPLY

Login before adding your answer.

Traffic: 291 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6