Is that possible to find if the sequence is enriched by specific motifs
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Liliian • 0
@67340e11
Last seen 19 months ago
United States

I'm wondering is that possible to find if the sequence is enriched by specific motifs?

For example, I have generated Granges object and DNAStringset :

> gr_up <-  GRanges(gr_up)
GRanges object with 376 ranges and 3 metadata columns:
      seqnames              ranges strand |            ENSG      pval      dPSI
         <Rle>           <IRanges>  <Rle> |     <character> <numeric> <numeric>
    1     chr1 167012370-167012510      + | ENSG00000143194 0.0000000  1.000000
    2     chr1 186304109-186304256      + | ENSG00000116690 0.0874126  0.666667
    3     chr1 154176116-154176178      - | ENSG00000143549 0.0000000  0.488313
    4     chr1 203347293-203348276      - | ENSG00000122176 0.0969031  0.482400
    5     chr1   54017377-54017426      - | ENSG00000203985 0.0289710  0.433965
  ...      ...                 ...    ... .             ...       ...       ...
  634     chrX   38804311-38804412      + | ENSG00000165175 0.0974026  0.134225
  635     chrX   68511850-68511976      + | ENSG00000181704 0.0309690  0.128942
  636     chrX   48575562-48575629      + | ENSG00000102317 0.0299700  0.119535
  637     chrX   47583409-47583535      + | ENSG00000102265 0.0109890  0.115762
  638     chrX 136548590-136549007      + | ENSG00000102243 0.0559441  0.100380
  -------
  seqinfo: 23 sequences from an unspecified genome; no seqlengths

> seqs_up <- getSeq(BSgenome.Hsapiens.UCSC.hg38, gr_up)
DNAStringSet object of length 376:
      width seq                                                                                                          names               
  [1]   141 TCCCCTAGTCTCCTGATGCTTCTTGTCATAATTCTTCTTGGACTAATTCACTG...TAATCAACAAATATTTATTGAGCACCTCCTCTGTGCCAGAAGATGATCCAAA 1
  [2]   148 GCATAATCCCACATCACCACCATCTTCAAAGAAAGCACCTCCACCTTCAGGAG...ACCAAACAAGAAGAAGACTAAGAAAGTTATAGAATCAGAGGAAATAACAGAA 2
  [3]    63 AGAGTGAGAGTAGTCGTCGAAAAAGTCGAAGAAGGTCGAAAACGTCCCGTCACCGGTCCGCGA                                              3
  [4]   984 TAACTAGGATAACGGAACCTCCATCTCCAAGAGGTCCAACCACAACTGACCCC...TCTCCCTCTTCTCGGGACGGTCGTCGTCCTCCCTCCAGGTGACGTAAAACAG 4
  [5]    50 AAGGGGAGGTCCCACCCGAAACCTAAGTCGTCGTCACATCGGTAAGAGAG                                                           5
  ...   ... ...
[372]   102 CACAGTCCAGCCACTGACCGCAGCAGCGCCCTTGCGTAGCAGCCGCTTGCAGCGAGAACACTGAATTGCCAACGAGCAGGAGAGTCTCAAGGCGCAAGAGGA       634
[373]   127 TTGCAGGCCTTTCAGATATATCCATCTCACAAGACATCCCCGTAGAAGGAGAA...GCATCCGGGAGTTTGACAGCTCCACATTAAATGAATCTGTTCGCAATACCAT 635
[374]    68 GGTCGTTGTCAAGGACCGGGAGACTCAGCGGTCCAGGGGTTTTGGTTTCATCACCTTCACCAACCCAG                                         636
[375]   127 ACCCACCATGGCCCCCTTTGAGCCCCTGGCTTCTGGCATCCTGTTGTTGCTGT...CTGCACCTGTGTCCCACCCCACCCACAGACGGCCTTCTGCAATTCCGACCTC 637
[376]   418 TGATAGCATGTCTCCAAATCAGTGGCGTTACTCGTCTCCATGGACAAAGCCAC...GATAGCTGGAAGCACAGGGTTGCTCTTCAACCTGCCTCCCGGCTCAGTTCAC 638

And then I have conducted motif enrichment analysis and found that these sequence set have some "C" enrich.

Motif Enrichment

I'm wondering is that possible to find which specific sequence(in Granges or DNAStringset ) has "C" enrich?

MotifDiscovery RNASeq • 693 views
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