Htykuut

I have GRanges object (coordinates of all gene exons); coding_pos defines what is the start position of a codon in a particular exon (1 means that first nucleotide in exon is also the first nt in a codon, and so on).

grTargetGene itself looks like this

> grTargetGene



GRanges object with 11 ranges and 7 metadata columns:

   seqnames                 ranges strand |     ensembl_ids   gene_biotype prev_exons_length coding_pos

      <Rle>              <IRanges>  <Rle> |     <character>    <character>         <numeric>  <numeric>

   [1]     chr2 [148602722, 148602776]      + | ENSG00000121989 protein_coding       0           1

   [2]     chr2 [148653870, 148654077]      + | ENSG00000121989 protein_coding       55          2

   [3]     chr2 [148657027, 148657136]      + | ENSG00000121989 protein_coding       263         3

   [4]     chr2 [148657313, 148657467]      + | ENSG00000121989 protein_coding       373         2

   [5]     chr2 [148672760, 148672903]      + | ENSG00000121989 protein_coding       528         1

   [6]     chr2 [148674852, 148674995]      + | ENSG00000121989 protein_coding       672         1

   [7]     chr2 [148676016, 148676161]      + | ENSG00000121989 protein_coding       816         1

   [8]     chr2 [148677799, 148677913]      + | ENSG00000121989 protein_coding       962         3

   [9]     chr2 [148680542, 148680680]      + | ENSG00000121989 protein_coding       1077        1

  [10]     chr2 [148683600, 148683730]      + | ENSG00000121989 protein_coding       1216        2

  [11]     chr2 [148684649, 148684843]      + | ENSG00000121989 protein_coding       1347        1

  -------

  seqinfo: 1 sequence from an unspecified genome; no seqlengths

I am interested in looking at coordinates separately for [1,2] positions in each codon and [3]. In other words, I would like to have 2 different GRanges objects that look approximately like this (here it is only the beginning)

> grTargetGene_Nonsynonym



GRanges object with X ranges and 7 metadata columns:

   seqnames                 ranges strand |     ensembl_ids   gene_biotype 

      <Rle>              <IRanges>  <Rle> |     <character>    <character> 

   [1]     chr2 [148602722, 148602723]      + | ENSG00000121989 protein_coding

   [2]     chr2 [148602725, 148602726]      + | ENSG00000121989 protein_coding

   [3]     chr2 [148602728, 148602729]      + | ENSG00000121989 protein_coding

   [4]     chr2 [148602731, 148602732]      + | ENSG00000121989 protein_coding







> grTargetGene_Synonym



GRanges object with X ranges and 7 metadata columns:

   seqnames                 ranges strand |     ensembl_ids   gene_biotype 

      <Rle>              <IRanges>  <Rle> |     <character>    <character> 

   [1]     chr2 [148602724, 148602724]      + | ENSG00000121989 protein_coding

   [2]     chr2 [148602727, 148602727]      + | ENSG00000121989 protein_coding

   [3]     chr2 [148602730, 148602730]      + | ENSG00000121989 protein_coding

   [4]     chr2 [148602733, 148602733]      + | ENSG00000121989 protein_coding

I was planning to do it through the loop that creates a set of granges for each exon according to coding_pos and strand, but I suspect there is a smarter way or maybe even a function that can do it already, but I couldn't find a simple solution.

Important: I do not need the sequence itself (the easiest way, in that case, would be to extract DNA first and then work with the sequence), but instead of doing this I only need the positions which I will use to overlap with some features.

> library("GenomicRanges")

> dput(grTargetGene)



new("GRanges"

, seqnames = new("Rle"

, values = structure(1L, .Label = "chr2", class = "factor")

, lengths = 6L

, elementMetadata = NULL

, metadata = list()

)

, ranges = new("IRanges"

, start = c(148602722L, 148653870L, 148657027L, 148657313L, 148672760L, 

148674852L)

, width = c(55L, 208L, 110L, 155L, 144L, 144L)

, NAMES = NULL

, elementType = "integer"

, elementMetadata = NULL

, metadata = list()

)

, strand = new("Rle"

, values = structure(1L, .Label = c("+", "-", "*"), class = "factor")

, lengths = 6L

, elementMetadata = NULL

, metadata = list()

)

, elementMetadata = new("DataFrame"

, rownames = NULL

, nrows = 6L

, listData = structure(list(ensembl_ids =

c("ENSG00000121989","ENSG00000121989", 

"ENSG00000121989", "ENSG00000121989", "ENSG00000121989", "ENSG00000121989"

), gene_biotype = c("protein_coding", "protein_coding", "protein_coding", 

"protein_coding", "protein_coding", "protein_coding"), cds_length =   

c(1542,1542, 1542, 1542, 1542, 1542), gene_start_position = c(148602086L, 

148602086L, 148602086L, 148602086L, 148602086L, 148602086L), 

gene_end_position = c(148688393L, 148688393L, 148688393L, 

148688393L, 148688393L, 148688393L), prev_exons_length = c(0, 

55, 263, 373, 528, 672), coding_pos = c(1, 2, 3, 2, 1, 1)), .Names =  

c("ensembl_ids", "gene_biotype", "cds_length", "gene_start_position",

"gene_end_position", 

"prev_exons_length", "coding_pos"))

, elementType = "ANY"

, elementMetadata = NULL

, metadata = list()

)

, seqinfo = new("Seqinfo"

, seqnames = "chr2"

, seqlengths = NA_integer_

, is_circular = NA

, genome = NA_character_

)

, metadata = list()

)

How about the following:

grl <- lapply(list(Nonsym = c(1, 2), Sym = c(3, 3)), function(x) {

    ranges(grTargetGene) <- IRanges(

        start = start(grTargetGene) + x[1] - 1,

        end = start(grTargetGene) + x[2] - 1)

    return(grTargetGene) })

grl

#$Nonsym

#GRanges object with 6 ranges and 7 metadata columns:

#      seqnames              ranges strand |     ensembl_ids   gene_biotype

#         <Rle>           <IRanges>  <Rle> |     <character>    <character>

#  [1]     chr2 148602722-148602723      + | ENSG00000121989 protein_coding

#  [2]     chr2 148653870-148653871      + | ENSG00000121989 protein_coding

#  [3]     chr2 148657027-148657028      + | ENSG00000121989 protein_coding

#  [4]     chr2 148657313-148657314      + | ENSG00000121989 protein_coding

#  [5]     chr2 148672760-148672761      + | ENSG00000121989 protein_coding

#  [6]     chr2 148674852-148674853      + | ENSG00000121989 protein_coding

#      cds_length gene_start_position gene_end_position prev_exons_length

#       <numeric>           <integer>         <integer>         <numeric>

#  [1]       1542           148602086         148688393                 0

#  [2]       1542           148602086         148688393                55

#  [3]       1542           148602086         148688393               263

#  [4]       1542           148602086         148688393               373

#  [5]       1542           148602086         148688393               528

#  [6]       1542           148602086         148688393               672

#      coding_pos

#       <numeric>

#  [1]          1

#  [2]          2

#  [3]          3

#  [4]          2

#  [5]          1

#  [6]          1

#  -------

#  seqinfo: 1 sequence from an unspecified genome; no seqlengths

#

#$Sym

#GRanges object with 6 ranges and 7 metadata columns:

#      seqnames    ranges strand |     ensembl_ids   gene_biotype cds_length

#         <Rle> <IRanges>  <Rle> |     <character>    <character>  <numeric>

#  [1]     chr2 148602724      + | ENSG00000121989 protein_coding       1542

#  [2]     chr2 148653872      + | ENSG00000121989 protein_coding       1542

#  [3]     chr2 148657029      + | ENSG00000121989 protein_coding       1542

#  [4]     chr2 148657315      + | ENSG00000121989 protein_coding       1542

#  [5]     chr2 148672762      + | ENSG00000121989 protein_coding       1542

#  [6]     chr2 148674854      + | ENSG00000121989 protein_coding       1542

#      gene_start_position gene_end_position prev_exons_length coding_pos

#                <integer>         <integer>         <numeric>  <numeric>

#  [1]           148602086         148688393                 0          1

#  [2]           148602086         148688393                55          2

#  [3]           148602086         148688393               263          3

#  [4]           148602086         148688393               373          2

#  [5]           148602086         148688393               528          1

#  [6]           148602086         148688393               672          1

#  -------

#  seqinfo: 1 sequence from an unspecified genome; no seqlengths

grl contains a list of two GRanges, one with ranges based on positions 1 and 2, and the other with ranges based on position 3.

I created a function that can account for a chain and allows to process exons that length is not divisible by 3 (and might be even less than 3)

CodonPosition_separation = function(grTargetGene) {

    grTargetGene = sort(grTargetGene)

    grTargetGene$prev_exons_length = c(0,width(grTargetGene)[1:length(grTargetGene)-1])

    if (length(grTargetGene) >1) {

        for (l in 2:length(grTargetGene)) {

          grTargetGene$prev_exons_length[l] = grTargetGene$prev_exons_length[l]+grTargetGene$prev_exons_length[l-1]

        }

      }

  grTargetGene$coding_pos =  grTargetGene$prev_exons_length%%3+1

  grTargetGene_N =  GRanges()

  grTargetGene_S =  GRanges()

  for (l in 1:length(grTargetGene)) {

    for (obj in c("start_nonsyn","start_syn", "end_nonsyn", "end_syn","gr_nonsyn","gr_syn")) {if(exists(obj)) {rm(obj)}}

    if (as.character(strand(grTargetGene)[1]) =="+"){

      start_ns = start(grTargetGene[l])+1-grTargetGene$coding_pos[l]

      end_ns = end(grTargetGene[l])

      if (start_ns <=end_ns) {

        start_nonsyn = seq(from = start(grTargetGene[l])+1-grTargetGene$coding_pos[l],to = end(grTargetGene[l]), by=3)

        end_nonsyn = seq(from = start(grTargetGene[l])+2-grTargetGene$coding_pos[l],to = end(grTargetGene[l]), by=3)

      }

      start_s =start(grTargetGene[l])+3-grTargetGene$coding_pos[l]

      end_s = end(grTargetGene[l])

      if (start_s <=end_s) {

        start_syn = seq(from = start(grTargetGene[l])+3-grTargetGene$coding_pos[l],to = end(grTargetGene[l]), by=3)

        end_syn = start_syn

      }



    } else {

      start_ns = end(grTargetGene[l])-1+grTargetGene$coding_pos[l]

      end_ns = start(grTargetGene[l])

      if (start_ns >=end_ns) {

        start_nonsyn = seq(from = end(grTargetGene[l])-1+grTargetGene$coding_pos[l],to = start(grTargetGene[l]), by=-3)

        end_nonsyn = seq(from = end(grTargetGene[l])-2+grTargetGene$coding_pos[l],to = start(grTargetGene[l]), by=-3)

      }

      start_s =end(grTargetGene[l])-3+grTargetGene$coding_pos[l]

      end_s = start(grTargetGene[l])

      if (start_ns >=end_ns) {

        start_syn = seq(from = end(grTargetGene[l])-3+grTargetGene$coding_pos[l],to = start(grTargetGene[l]), by=-3)

        end_syn = start_syn

      }

    }

    if (exists("start_nonsyn")) {

      length_nonsyn = length(start_nonsyn)+ length(end_nonsyn)

      gr_nonsyn = GRanges(

        seqnames = rep(seqnames(grTargetGene[l]), length_nonsyn),

        strand = rep(strand(grTargetGene[l]), length_nonsyn),

        ranges = IRanges(start = c(start_nonsyn, end_nonsyn), end = c(start_nonsyn, end_nonsyn))

      )

      gr_nonsyn = intersect(gr_nonsyn,grTargetGene[l])

      grTargetGene_N = append(grTargetGene_N, gr_nonsyn)

      } 

    if (exists("start_syn")) {

      length_syn = length(start_syn)

      gr_syn = GRanges(

        seqnames = rep(seqnames(grTargetGene[l]), length_syn),

        strand = rep(strand(grTargetGene[l]), length_syn),

        ranges = IRanges(start = start_syn, end = end_syn)

      )

      gr_syn = intersect(gr_syn,grTargetGene[l])

      grTargetGene_S = append(grTargetGene_S, gr_syn)

    }

  }

  return(list("grTargetGene_S"=grTargetGene_S,"grTargetGene_N"=grTargetGene_N))

}

It works nicely:

> CodonPosition_separation(grTargetGene)

$grTargetGene_S

GRanges object with 514 ranges and 0 metadata columns:

        seqnames                 ranges strand

           <Rle>              <IRanges>  <Rle>

    [1]     chr2 [148602724, 148602724]      +

    [2]     chr2 [148602727, 148602727]      +

    [3]     chr2 [148602730, 148602730]      +

    [4]     chr2 [148602733, 148602733]      +

    [5]     chr2 [148602736, 148602736]      +

    ...      ...                    ...    ...

  [510]     chr2 [148684831, 148684831]      +

  [511]     chr2 [148684834, 148684834]      +

  [512]     chr2 [148684837, 148684837]      +

  [513]     chr2 [148684840, 148684840]      +

  [514]     chr2 [148684843, 148684843]      +

  -------

  seqinfo: 1 sequence from an unspecified genome; no seqlengths



$grTargetGene_N

GRanges object with 517 ranges and 0 metadata columns:

        seqnames                 ranges strand

           <Rle>              <IRanges>  <Rle>

    [1]     chr2 [148602722, 148602723]      +

    [2]     chr2 [148602725, 148602726]      +

    [3]     chr2 [148602728, 148602729]      +

    [4]     chr2 [148602731, 148602732]      +

    [5]     chr2 [148602734, 148602735]      +

    ...      ...                    ...    ...

  [513]     chr2 [148684829, 148684830]      +

  [514]     chr2 [148684832, 148684833]      +

  [515]     chr2 [148684835, 148684836]      +

  [516]     chr2 [148684838, 148684839]      +

  [517]     chr2 [148684841, 148684842]      +

  -------

  seqinfo: 1 sequence from an unspecified genome; no seqlengths