Question

GenomicRanges: Find first, second and third nearest genes

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ssabri ▴ 20

@ssabri-9464

Last seen 4.7 years ago

For each row of signal, I'd like to find what the nearest n genes are and their corresponding distances.

>signal
GRanges object with 295644 ranges and 1 metadata column:
           seqnames            ranges strand |      E123
              <Rle>         <IRanges>  <Rle> | <numeric>
       [1]    chr19             1-200      * |         0
       [2]    chr19           201-400      * |         0
       [3]    chr19           401-600      * |         0
       [4]    chr19           601-800      * |         0
       [5]    chr19          801-1000      * |         0
       ...      ...               ...    ... .       ...
  [295640]    chr19 59127801-59128000      * |         0
  [295641]    chr19 59128001-59128200      * |         0
  [295642]    chr19 59128201-59128400      * |         0
  [295643]    chr19 59128401-59128600      * |         0
  [295644]    chr19 59128601-59128800      * |         0
  -------
  seqinfo: 23 sequences from an unspecified genome

>genes
GRanges object with 18436 ranges and 5 metadata columns:
          seqnames    ranges strand |         gene_id      gene_type   gene_name                                                                        gene_description               Expr
             <Rle> <IRanges>  <Rle> |     <character>    <character> <character>                                                                             <character>          <numeric>
    OR4F5     chr1     69091      + | ENSG00000186092 protein_coding       OR4F5      olfactory_receptor,_family_4,_subfamily_F,_member_5_[Source:HGNC_Symbol;Acc:14825]                  0
   SAMD11     chr1    860260      + | ENSG00000187634 protein_coding      SAMD11                 sterile_alpha_motif_domain_containing_11_[Source:HGNC_Symbol;Acc:28706]  0.420768029336243
   KLHL17     chr1    895967      + | ENSG00000187961 protein_coding      KLHL17                               kelch-like_17_(Drosophila)_[Source:HGNC_Symbol;Acc:24023]   3.02720360347554
  PLEKHN1     chr1    901877      + | ENSG00000187583 protein_coding     PLEKHN1 pleckstrin_homology_domain_containing,_family_N_member_1_[Source:HGNC_Symbol;Acc:25284]  0.841240518732754
    ISG15     chr1    948803      + | ENSG00000187608 protein_coding       ISG15                             ISG15_ubiquitin-like_modifier_[Source:HGNC_Symbol;Acc:4053]   1.16774328010894
      ...      ...       ...    ... .             ...            ...         ...                                                                                     ...                ...
  MTCP1NB     chrX 154299637      - | ENSG00000182712 protein_coding     MTCP1NB                   mature_T-cell_proliferation_1_neighbor_[Source:HGNC_Symbol;Acc:35428]     4.872993207549
    MTCP1     chrX 154376212      - | ENSG00000214827 protein_coding       MTCP1                             mature_T-cell_proliferation_1_[Source:HGNC_Symbol;Acc:7423]   2.00656014504748
   RAB39B     chrX 154493874      - | ENSG00000155961 protein_coding      RAB39B                       RAB39B,_member_RAS_oncogene_family_[Source:HGNC_Symbol;Acc:16499] 0.0983656544592598
    CLIC2     chrX 154563966      - | ENSG00000155962 protein_coding       CLIC2                          chloride_intracellular_channel_2_[Source:HGNC_Symbol;Acc:2063]   1.46184283788407
    TMLHE     chrX 154899605      - | ENSG00000185973 protein_coding       TMLHE                     trimethyllysine_hydroxylase,_epsilon_[Source:HGNC_Symbol;Acc:18308]   1.34060784208875
  -------
  seqinfo: 23 sequences from hg19 genome

I've explored distanceToNearest(signal, genes, select = "all") which returns:

Hits object with 295913 hits and 1 metadata column:
           queryHits subjectHits |  distance
           <integer>   <integer> | <integer>
       [1]         1       15215 |    107265
       [2]         2       15215 |    107065
       [3]         3       15215 |    106865
       [4]         4       15215 |    106665
       [5]         5       15215 |    106465
       ...       ...         ... .       ...
  [295909]    295640       16535 |     42858
  [295910]    295641       16535 |     43058
  [295911]    295642       16535 |     43258
  [295912]    295643       16535 |     43458
  [295913]    295644       16535 |     43658
  -------
  queryLength: 295644 / subjectLength: 18436

But I'd like to expand this to several genes, not just the closest.

Any help would be much appreciated!

R GenomicRanges Granges • 2.5k views

ADD COMMENT • link updated 4.8 years ago by Gordon Smyth 52k • written 4.8 years ago by ssabri ▴ 20

score 0 · Answer 1 · 2020-02-25

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

See https://support.bioconductor.org/p/127895/#128144

ADD COMMENT • link 4.8 years ago Michael Lawrence ★ 11k

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Great -- I'll have a look and see if I can get this to work. I will report back!

ADD REPLY • link 4.8 years ago ssabri ▴ 20

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Hmm any ideas on this error?

>GenomicRanges:::findKNN(signal, genes, k = 2) # get the 2 nearest genes for every location in signal

Error in pc(extractList(start(starts), pwindows) - end(query), end(query) -  : 
  all the objects to combine must have the same length

ADD REPLY • link 4.8 years ago ssabri ▴ 20

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If I swap genes and signal, it returns:

> GenomicRanges:::findKNN(genes, signal, k = 2)
IntegerList of length 18436
[[1]] integer(0)
[[2]] integer(0)
[[3]] integer(0)
[[4]] integer(0)
[[5]] integer(0)
[[6]] integer(0)
[[7]] integer(0)
[[8]] integer(0)
[[9]] integer(0)
[[10]] integer(0)
...
<18426 more elements>

ADD REPLY • link 4.8 years ago ssabri ▴ 20

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The function seems to break at this line within GenomicRanges:::findKNN():

dist <- pc(extractList(start(starts), pwindows) - end(query), end(query) - extractList(end(ends), fwindows)) # ERRORS OUT

any help would be much appreciated!

ADD REPLY • link 4.8 years ago ssabri ▴ 20

score 0 · Answer 2 · 2020-02-26

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Gordon Smyth 52k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

csaw::detailRanges may also be of interest.

ADD COMMENT • link 4.8 years ago Gordon Smyth 52k