Question

Obtain the specific range that overlap

0

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julrodr80 ▴ 30

@julrodr80-11991

Last seen 7.1 years ago

I have two dataframes: cnv_1

chr     start   end
3   62860387    63000898
12  31296219    31406907
14  39762575    39769146
19  43372386    43519442
19  56419263    56572829

cnv_2

chr     start   end
6   30994163    30995078
19  43403531    44608011
18  1731154 1833682
3   46985863    47164711

with aprox 150000 entries each. I would like to know which fragments of cnv_1overlap in any way with cnv_2, and -this is the most important for me- to obtain the specific region that overlap. For example, doing that to the data.frames of the example, to obtain:

chr     start   end
19  43403531 43519442

thank you very much

overlap genomicranges range • 1.5k views

ADD COMMENT • link 7.9 years ago julrodr80 ▴ 30

score 1 · Answer 1 · 2016-12-07

1

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.9 years ago

United States

First make them GRanges,

cnv_gr_1 <- GRanges(cnv_1)
cnv_gr_2 <- GRanges(cnv_2)

And then find overlaps and the intersecting part of each overlapping pair:

pintersect(findOverlapPairs(cnv_gr_1, cnv_gr_2))

ADD COMMENT • link 7.9 years ago Michael Lawrence ★ 11k

0

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I don't know why but...

findOverlapPairs()
Error: could not find function "findOverlapPairs"

ADD REPLY • link 7.9 years ago julrodr80 ▴ 30

0

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You'll need to update your Biocondutor.

ADD REPLY • link 7.9 years ago Michael Lawrence ★ 11k

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I have this problem

Error: Bioconductor version 3.2 cannot be upgraded with R version 3.2.3

It's very frustrating, is the only function that does't work.

ADD REPLY • link 7.9 years ago julrodr80 ▴ 30

0

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You'd need to update your R, and then your Bioconductor installation (in that order). It'll always help if you post your `sessionInfo()` along with your post, that way everyone knows exactly what platform and what versions of package you have installed.

If you want a copy of all the packages you have installed in your current R, to carry over to the new installation of R, you can do something like this in R,

write.csv(rownames(installed.packages()),file="rpacks.txt")

These can be installed in an R script (on a new R installation) or interactively with,

library(BiocInstaller)

lst <- unlist(read.csv("rpacks.txt"))

lapply(as.character(lst), biocLite, ask=FALSE)

Also, please take a look at the documentation for this,

http://bioconductor.org/install/

ADD REPLY • link 7.9 years ago nitesh.turaga ▴ 140