Question: the closest gene to a breakpoint
0
gravatar for Bogdan
16 months ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Dear all, please would you advise :

given a list of chromosomes coordinates (i.e. BREAKPOINTS), and the list of genes promoters( i.e. TSS), how shall I get the closest gene TSS to a BREAKPOINT ? which function shall I use ?

I am looking for a similar function as closestBed in bedtools  ...

thanks a lot,

-- bogdan

granges plyranges • 401 views
ADD COMMENTlink modified 16 months ago by Gordon Smyth39k • written 16 months ago by Bogdan580
Answer: the closest gene to a breakpoint
2
gravatar for Michael Lawrence
16 months ago by
United States
Michael Lawrence11k wrote:

If you know of something that works in bedtools, then just use HelloRanges to find the equivalent. It's going to be based on nearest().

ADD COMMENTlink written 16 months ago by Michael Lawrence11k

Another option is to use join_nearest() or pair_nearest() from plyranges

ADD REPLYlink modified 16 months ago • written 16 months ago by lee.s70
Answer: the closest gene to a breakpoint
1
gravatar for Julie Zhu
16 months ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:
Bogdan, AnnotatePeakInBatch in the ChIPpeakAnno package should do. https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html Best regards, Julie
ADD COMMENTlink modified 16 months ago • written 16 months ago by Julie Zhu4.1k

Thank you Julie. I believe that I shall use the function " annoPeaks " ?

ADD REPLYlink written 16 months ago by Bogdan580
Bogdan, The function annoPeaks works as well. Best, Julie Activity
ADD REPLYlink written 16 months ago by Julie Zhu4.1k
Answer: the closest gene to a breakpoint
1
gravatar for Gordon Smyth
16 months ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:
> library(edgeR)
> nearestTSS(chr="chr6", locus=300000, species="Hs")
      gene_id symbol width    tss strand distance
20824   56940 DUSP22 59299 292057      +    -7943

 

ADD COMMENTlink written 16 months ago by Gordon Smyth39k

Thank you Gordon. Happy to see that edgeR expands its set of functions ...

ADD REPLYlink written 16 months ago by Bogdan580
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