The functions has* can be used to subset the GRanges object containing
information about tRNAs.
Please not that the settings mismatches and bulged take
precedence before unpaired or paired. This means that by
setting either mismatches or bulged to either TRUE or
FALSE, unpaired = TRUE or paired = TRUE are
automatically set to allow specific subsetting. If this removes elements from
the results, please consider constructing a logical vectors with two calls as
suggested in the examples.
hasTStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
hasDStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
hasAcceptorStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
hasAnticodonStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
hasTloop(x, length = NA)
hasDloop(x, length = NA)
hasAnticodonLoop(x, length = NA)
hasVariableLoop(x, length = NA, paired = NA, mismatches = NA, bulged = NA)
# S4 method for GRanges
hasTStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
# S4 method for GRanges
hasDStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
# S4 method for GRanges
hasAcceptorStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
# S4 method for GRanges
hasAnticodonStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA)
# S4 method for GRanges
hasTloop(x, length = NA)
# S4 method for GRanges
hasDloop(x, length = NA)
# S4 method for GRanges
hasAnticodonLoop(x, length = NA)
# S4 method for GRanges
hasVariableLoop(x, length = NA, paired = NA, mismatches = NA, bulged = NA)a GRanges object from a tRNAscan import or with equivalent information
the length as integer
logical: has unpaired nucleotides
logical: has mismatched nucleotides
logical: has mismatched nucleotides of different length creating a bulge
logical: has paired nucleotides (only used for loops)
a logical vector of the length or input GRanges object
data("gr", package = "tRNA")
hasTStem(gr, length = 5, mismatches = TRUE)
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [25] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [49] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [61] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [97] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [133] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
#> [157] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [169] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [181] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [193] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [205] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [217] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
#> [229] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [241] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [253] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [265] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
#> [277] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [289] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
gr[hasTStem(gr, length = 5, mismatches = TRUE)]
#> GRanges object with 11 ranges and 18 metadata columns:
#> seqnames ranges strand | no tRNA_length tRNA_type
#> <Rle> <IRanges> <Rle> | <integer> <integer> <character>
#> [1] chrIII 227942-228042 + | 4 81 Ser
#> [2] chrIV 1175829-1175901 + | 12 72 Met
#> [3] chrV 288443-288524 - | 17 81 Ser
#> [4] chrIX 248850-248931 + | 4 81 Ser
#> [5] chrX 391043-391115 - | 19 72 Met
#> [6] chrX 422937-423009 + | 8 72 Met
#> [7] chrXIII 572883-572955 - | 12 72 Met
#> [8] chrXIII 808246-808317 - | 8 70 Gln
#> [9] chrXV 976421-976493 + | 12 72 Met
#> [10] chrXVI 689565-689646 + | 3 81 Ser
#> [11] chrmt 731-802 + | 1 71 Pro
#> tRNA_anticodon tRNA_anticodon.start tRNA_anticodon.end tRNAscan_score
#> <character> <integer> <integer> <numeric>
#> [1] CGA 34 36 71.6
#> [2] CAT 34 36 69.9
#> [3] TGA 34 36 80.1
#> [4] TGA 34 36 80.1
#> [5] CAT 34 36 69.9
#> [6] CAT 34 36 69.9
#> [7] CAT 34 36 69.9
#> [8] CTG 34 36 59.9
#> [9] CAT 34 36 69.9
#> [10] TGA 34 36 80.1
#> [11] TGG 33 35 37.0
#> tRNA_seq tRNA_str tRNA_CCA.end
#> <RNAStringSet> <DotBracketStringSet> <logical>
#> [1] GGCACUAUGG...GCUGGUGUCG <<<<<<<..<...>>>>>>>>>. FALSE
#> [2] GCUUCAGUAG...CCCUGGAGCA <<<<<<<..<....>>>>>>>>. FALSE
#> [3] GGCACUAUGG...GCUGGUGUCG <<<<<<<..<...>>>>>>>>>. FALSE
#> [4] GGCACUAUGG...GCUGGUGUCG <<<<<<<..<...>>>>>>>>>. FALSE
#> [5] GCUUCAGUAG...CCCUGGAGCA <<<<<<<..<....>>>>>>>>. FALSE
#> [6] GCUUCAGUAG...CCCUGGAGCA <<<<<<<..<....>>>>>>>>. FALSE
#> [7] GCUUCAGUAG...CCCUGGAGCA <<<<<<<..<....>>>>>>>>. FALSE
#> [8] GGUCCUAUAG...GGUGGGACCU <<<<<<<..<...>>>>>>>>>. FALSE
#> [9] GCUUCAGUAG...CCCUGGAGCA <<<<<<<..<....>>>>>>>>. FALSE
#> [10] GGCACUAUGG...GCUGGUGUCG <<<<<<<..<...>>>>>>>>>. FALSE
#> [11] CAGAUAGAAG...UCCUAUCUGA <<<<<<<..<....>>>>>>>>. FALSE
#> tRNAscan_potential.pseudogene tRNAscan_intron.start tRNAscan_intron.end
#> <logical> <integer> <integer>
#> [1] FALSE 227979 227997
#> [2] FALSE <NA> <NA>
#> [3] FALSE <NA> <NA>
#> [4] FALSE <NA> <NA>
#> [5] FALSE <NA> <NA>
#> [6] FALSE <NA> <NA>
#> [7] FALSE <NA> <NA>
#> [8] FALSE <NA> <NA>
#> [9] FALSE <NA> <NA>
#> [10] FALSE <NA> <NA>
#> [11] FALSE <NA> <NA>
#> tRNAscan_intron.locstart tRNAscan_intron.locend tRNAscan_hmm.score
#> <integer> <integer> <numeric>
#> [1] 38 56 48.7
#> [2] <NA> <NA> 53.7
#> [3] <NA> <NA> 58.0
#> [4] <NA> <NA> 58.0
#> [5] <NA> <NA> 53.7
#> [6] <NA> <NA> 53.7
#> [7] <NA> <NA> 53.7
#> [8] <NA> <NA> 36.7
#> [9] <NA> <NA> 53.7
#> [10] <NA> <NA> 58.0
#> [11] <NA> <NA> NA
#> tRNAscan_sec.str.score tRNAscan_infernal
#> <numeric> <numeric>
#> [1] 22.9 NA
#> [2] 16.2 NA
#> [3] 22.1 NA
#> [4] 22.1 NA
#> [5] 16.2 NA
#> [6] 16.2 NA
#> [7] 16.2 NA
#> [8] 23.2 NA
#> [9] 16.2 NA
#> [10] 22.1 NA
#> [11] NA NA
#> -------
#> seqinfo: 17 sequences from an unspecified genome; no seqlengths
gr[hasDStem(gr, unpaired = FALSE) & hasDStem(gr, mismatches = FALSE)]
#> GRanges object with 298 ranges and 18 metadata columns:
#> seqnames ranges strand | no tRNA_length tRNA_type
#> <Rle> <IRanges> <Rle> | <integer> <integer> <character>
#> [1] chrI 139152-139254 + | 1 71 Pro
#> [2] chrI 166267-166339 + | 2 72 Ala
#> [3] chrI 181141-181254 + | 3 80 Leu
#> [4] chrI 182522-182603 - | 4 81 Ser
#> [5] chrII 9583-9666 + | 1 82 Leu
#> ... ... ... ... . ... ... ...
#> [294] chrmt 72632-72705 + | 20 72 Met
#> [295] chrmt 77431-77502 + | 21 71 Phe
#> [296] chrmt 78091-78162 - | 24 71 Sup
#> [297] chrmt 78533-78605 + | 22 72 Val
#> [298] chrmt 85035-85107 + | 23 72 Met
#> tRNA_anticodon tRNA_anticodon.start tRNA_anticodon.end tRNAscan_score
#> <character> <integer> <integer> <numeric>
#> [1] TGG 33 35 62.1
#> [2] TGC 34 36 76.0
#> [3] CAA 35 37 57.5
#> [4] AGA 34 36 83.1
#> [5] TAA 35 37 75.2
#> ... ... ... ... ...
#> [294] CAT 35 37 61.2
#> [295] GAA 33 35 60.1
#> [296] TTA 33 35 51.3
#> [297] TAC 34 36 64.6
#> [298] CAT 35 37 51.2
#> tRNA_seq tRNA_str tRNA_CCA.end
#> <RNAStringSet> <DotBracketStringSet> <logical>
#> [1] GGGCGUGUGG...AGCUCGCCCC <<<<<.<..<...>>>.>>>>>. FALSE
#> [2] GGGCACAUGG...GUUGCGUCCA <<<<.<<..<...>>>>.>>>>. FALSE
#> [3] GGUUGUUUGG...UUAGCAACCA <<<<<<<..<...>>>>>>>>>. FALSE
#> [4] GGCAACUUGG...GCAGUUGUCG <<<<<<<..<...>>>>>>>>>. FALSE
#> [5] GGAGGGUUGG...GCAUCCUUCA <<<<<<<..<...>>>>>>>>>. FALSE
#> ... ... ... ...
#> [294] GCUUGUAUAG...UCUACAAGUA <<<<<<<..<...>.>>>>>>>. FALSE
#> [295] GCUUUUAUAG...AUUAAGGGCA <<<<<<<..<...>>>>>>>>>. FALSE
#> [296] GUAAAUAUAA...AGUAUUUACA <<<<<<<..<...>>>>>>>>>. FALSE
#> [297] AGGAGAUUAG...AUAUUUCCUA <<<<<<<..<...>>>>>>>>>. FALSE
#> [298] UGCAAUAUGA...AUUAUUGCUA .<<<<<<..<...>>>>>>>>.. FALSE
#> tRNAscan_potential.pseudogene tRNAscan_intron.start tRNAscan_intron.end
#> <logical> <integer> <integer>
#> [1] FALSE 139188 139218
#> [2] FALSE <NA> <NA>
#> [3] FALSE 181179 181210
#> [4] FALSE <NA> <NA>
#> [5] FALSE <NA> <NA>
#> ... ... ... ...
#> [294] FALSE <NA> <NA>
#> [295] FALSE <NA> <NA>
#> [296] FALSE <NA> <NA>
#> [297] FALSE <NA> <NA>
#> [298] FALSE <NA> <NA>
#> tRNAscan_intron.locstart tRNAscan_intron.locend tRNAscan_hmm.score
#> <integer> <integer> <numeric>
#> [1] 37 67 37.9
#> [2] <NA> <NA> 53.4
#> [3] 39 70 27.0
#> [4] <NA> <NA> 49.7
#> [5] <NA> <NA> 45.3
#> ... ... ... ...
#> [294] <NA> <NA> NA
#> [295] <NA> <NA> NA
#> [296] <NA> <NA> NA
#> [297] <NA> <NA> NA
#> [298] <NA> <NA> NA
#> tRNAscan_sec.str.score tRNAscan_infernal
#> <numeric> <numeric>
#> [1] 24.2 NA
#> [2] 22.6 NA
#> [3] 30.5 NA
#> [4] 33.4 NA
#> [5] 29.9 NA
#> ... ... ...
#> [294] NA NA
#> [295] NA NA
#> [296] NA NA
#> [297] NA NA
#> [298] NA NA
#> -------
#> seqinfo: 17 sequences from an unspecified genome; no seqlengths