gettRNAstructureSeqs: tRNA structures and sequences

In tRNA: Analyzing tRNA sequences and structures

Description

gettRNAstructureGRanges returns a list of GRanges describing the boundaries of tRNA structures as extracted from the dot bracket annotation. The dot bracket annotation is parsed using gettRNABasePairing, which internally uses getBasePairing.

gettRNAstructureSeq returns split or partial tRNA sequences based on the structure information. Variations in the ength of structure features can be padded to retrieve sequences of equal length. If sequences are joined by setting joinCompletely = FALSE, the boundaries of the tRNA structure are stored in the result as metadata. They can be accessesed as an IRanges object by using metadata(seq)[["tRNA_structures"]].

Usage

gettRNAstructureGRanges(x, structure = "")

gettRNAstructureSeqs(
  x,
  structure = "",
  joinCompletely = FALSE,
  joinFeatures = FALSE,
  padSequences = TRUE
)

## S4 method for signature 'GRanges'
gettRNAstructureSeqs(
  x,
  structure = "",
  joinCompletely = FALSE,
  joinFeatures = FALSE,
  padSequences = TRUE
)

## S4 method for signature 'GRanges'
gettRNAstructureGRanges(x, structure = "")

Arguments

x	a GRanges object with tRNA information. It has to pass the istRNAGRanges function.
structure	optional parameter for returning just partial sequences. The following values are accepted: anticodonStem, Dprime5, DStem, Dloop, Dprime3, acceptorStem, anticodonloop, variableLoop, TStem, Tloop, discriminator. (default: structure = "")
joinCompletely	Should the sequence parts, which are to be returned, be joined into one sequence? (default: joinCompletely = FALSE)) Setting this to TRUE excludes joinFeatures be set to TRUE as well. In addition, joinCompletely = TRUE uses automatically all sequence structures.
joinFeatures	Should the sequence parts, which are to be returned and are from the same structure type, be joined into one sequence? (default: joinCompletely = FALSE)) Setting this to TRUE excludes joinCompletely be set to TRUE as well. joinCompletely takes precedence.
padSequences	parameter whether sequences of the same type should be returned with the same length. For stems missing positions will be filled up in the middle, for loops at the ends. (default: padSequences = TRUE). If joinCompletely == TRUE this is set to TRUE automatically.

Value

a list of GRanges or DNAStringSet objects. In case joinCompletly is set to TRUE a single DNAStringSet is returned.

Examples

data("gr", package = "tRNA")
gettRNAstructureGRanges(gr, structure = "anticodonLoop")
gettRNAstructureSeqs(gr, structure = "anticodonLoop")
gettRNABasePairing(gr[1:10])

Example output

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Structstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

There were 50 or more warnings (use warnings() to see the first 50)
$anticodonLoop
IRanges object with 299 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  TGG        31        37         7
  TGC        32        38         7
  CAA        31        37         7
  AGA        31        37         7
  TAA        31        37         7
  ...       ...       ...       ...
  CAT        32        38         7
  GAA        31        37         7
  TTA        31        37         7
  TAC        32        38         7
  CAT        32        38         7

$anticodonLoop
RNAStringSet object of length 299:
      width seq                                             names               
  [1]     7 UUUGGGU                                         TGG
  [2]     7 CUUGCAA                                         TGC
  [3]     7 UUCAAGC                                         CAA
  [4]     7 UUAGAAA                                         AGA
  [5]     7 CUUAAGA                                         TAA
  ...   ... ...
[295]     7 CUCAUAA                                         CAT
[296]     7 UUGAAGA                                         GAA
[297]     7 UUUUAGU                                         TTA
[298]     7 UUUACAC                                         TAC
[299]     7 GUCAUGA                                         CAT

SplitDotBracketDataFrameList of length 10
[[1]]
DotBracketDataFrame with 71 rows and 4 columns
          pos   forward   reverse   character
    <integer> <integer> <integer> <character>
1           1         1        70           <
2           2         2        69           <
3           3         3        68           <
4           4         4        67           <
5           5         5        66           <
...       ...       ...       ...         ...
67         67        67         4           >
68         68        68         3           >
69         69        69         2           >
70         70        70         1           >
71         71         0         0           .

...
<9 more elements>

tRNA documentation built on Nov. 8, 2020, 11:08 p.m.