Question

the closest gene to a breakpoint

0

Entering edit mode

Bogdan ▴ 670

@bogdan-2367

Last seen 13 months ago

Palo Alto, CA, USA

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 • 1.7k views

ADD COMMENT • link updated 6.2 years ago by Gordon Smyth 51k • written 6.3 years ago by Bogdan ▴ 670

score 2 · Answer 1 · 2018-08-27

2

Entering edit mode

Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

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 COMMENT • link 6.3 years ago Michael Lawrence ★ 11k

0

Entering edit mode

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

ADD REPLY • link 6.2 years ago lee.s ▴ 70

score 1 · Answer 2 · 2018-08-27

1

Entering edit mode

Julie Zhu ★ 4.3k

@julie-zhu-3596

Last seen 13 months ago

United States

Bogdan, AnnotatePeakInBatch in the ChIPpeakAnno package should do. https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html Best regards, Julie

ADD COMMENT • link 6.3 years ago Julie Zhu ★ 4.3k

0

Entering edit mode

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

ADD REPLY • link 6.3 years ago Bogdan ▴ 670

0

Entering edit mode

Bogdan, The function annoPeaks works as well. Best, Julie Activity

ADD REPLY • link 6.3 years ago Julie Zhu ★ 4.3k

score 1 · Answer 3 · 2018-08-28

1

Entering edit mode

Gordon Smyth 51k

@gordon-smyth

Last seen 9 hours ago

WEHI, Melbourne, Australia

> library(edgeR)
> nearestTSS(chr="chr6", locus=300000, species="Hs")
      gene_id symbol width    tss strand distance
20824   56940 DUSP22 59299 292057      +    -7943