gettRNASummary prepares a DataFrame with the aggregated features
of tRNAs from a GRanges object. Logical values are converted to numeric
values.
gettRNASummary(x)
# S4 method for GRangesList
gettRNASummary(x)
# S4 method for GRanges
gettRNASummary(x)a GRanges or a GRangesList object. All elements have to pass the
istRNAGRanges test.
a DataFrame object
data("gr", package = "tRNA")
gettRNASummary(gr)
#> DataFrame with 299 rows and 39 columns
#> gc width length cca features_all_valid
#> <numeric> <integer> <integer> <logical> <logical>
#> 1 0.605634 103 71 FALSE TRUE
#> 2 0.611111 73 72 FALSE TRUE
#> 3 0.500000 114 80 FALSE TRUE
#> 4 0.543210 82 81 FALSE TRUE
#> 5 0.585366 84 82 FALSE TRUE
#> ... ... ... ... ... ...
#> 295 0.263889 74 72 FALSE TRUE
#> 296 0.323944 72 71 FALSE TRUE
#> 297 0.197183 72 71 FALSE TRUE
#> 298 0.347222 73 72 FALSE TRUE
#> 299 0.291667 73 72 FALSE TRUE
#> features_Dstem_found features_Tstem_found acceptorStem_length
#> <logical> <logical> <integer>
#> 1 TRUE TRUE 7
#> 2 TRUE TRUE 7
#> 3 TRUE TRUE 7
#> 4 TRUE TRUE 7
#> 5 TRUE TRUE 7
#> ... ... ... ...
#> 295 TRUE TRUE 7
#> 296 TRUE TRUE 7
#> 297 TRUE TRUE 7
#> 298 TRUE TRUE 7
#> 299 TRUE TRUE 6
#> Dprime5_length DStem_length Dloop_length Dprime3_length
#> <integer> <integer> <integer> <integer>
#> 1 2 3 9 1
#> 2 2 4 8 1
#> 3 2 3 9 1
#> 4 2 3 9 1
#> 5 2 3 9 1
#> ... ... ... ... ...
#> 295 2 4 8 1
#> 296 2 4 7 1
#> 297 2 4 7 1
#> 298 2 3 10 1
#> 299 2 4 8 1
#> anticodonStem_length anticodonLoop_length variableLoop_length TStem_length
#> <integer> <integer> <integer> <integer>
#> 1 5 7 4 5
#> 2 5 7 4 5
#> 3 5 7 13 5
#> 4 5 7 14 5
#> 5 5 7 15 5
#> ... ... ... ... ...
#> 295 5 7 4 4
#> 296 5 7 4 5
#> 297 5 7 4 5
#> 298 5 7 4 5
#> 299 5 7 4 5
#> Tloop_length discriminator_length acceptorStem_unpaired DStem_unpaired
#> <integer> <integer> <logical> <logical>
#> 1 7 1 TRUE FALSE
#> 2 7 1 TRUE FALSE
#> 3 7 1 FALSE FALSE
#> 4 7 1 FALSE FALSE
#> 5 7 1 FALSE FALSE
#> ... ... ... ... ...
#> 295 7 1 FALSE FALSE
#> 296 7 1 FALSE FALSE
#> 297 7 1 FALSE FALSE
#> 298 7 1 FALSE FALSE
#> 299 7 1 FALSE FALSE
#> anticodonStem_unpaired variableLoop_unpaired TStem_unpaired
#> <logical> <logical> <logical>
#> 1 FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE
#> 3 FALSE FALSE FALSE
#> 4 FALSE FALSE FALSE
#> 5 FALSE FALSE FALSE
#> ... ... ... ...
#> 295 FALSE FALSE FALSE
#> 296 FALSE FALSE FALSE
#> 297 FALSE FALSE FALSE
#> 298 FALSE FALSE FALSE
#> 299 FALSE FALSE FALSE
#> acceptorStem_mismatches DStem_mismatches anticodonStem_mismatches
#> <logical> <logical> <logical>
#> 1 TRUE FALSE FALSE
#> 2 TRUE FALSE FALSE
#> 3 FALSE FALSE FALSE
#> 4 FALSE FALSE FALSE
#> 5 FALSE FALSE FALSE
#> ... ... ... ...
#> 295 FALSE FALSE FALSE
#> 296 FALSE FALSE FALSE
#> 297 FALSE FALSE FALSE
#> 298 FALSE FALSE FALSE
#> 299 FALSE FALSE FALSE
#> variableLoop_mismatches TStem_mismatches acceptorStem_bulges DStem_bulges
#> <logical> <logical> <logical> <logical>
#> 1 FALSE FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE FALSE
#> 3 FALSE FALSE FALSE FALSE
#> 4 FALSE FALSE FALSE FALSE
#> 5 FALSE FALSE FALSE FALSE
#> ... ... ... ... ...
#> 295 FALSE FALSE FALSE FALSE
#> 296 FALSE FALSE FALSE FALSE
#> 297 FALSE FALSE FALSE FALSE
#> 298 FALSE FALSE FALSE FALSE
#> 299 FALSE FALSE FALSE FALSE
#> anticodonStem_bulges variableLoop_bulges TStem_bulges tRNAscan_score
#> <logical> <logical> <logical> <numeric>
#> 1 FALSE FALSE FALSE 62.1
#> 2 FALSE FALSE FALSE 76.0
#> 3 FALSE FALSE FALSE 57.5
#> 4 FALSE FALSE FALSE 83.1
#> 5 FALSE FALSE FALSE 75.2
#> ... ... ... ... ...
#> 295 FALSE FALSE FALSE 61.2
#> 296 FALSE FALSE FALSE 60.1
#> 297 FALSE FALSE FALSE 51.3
#> 298 FALSE FALSE FALSE 64.6
#> 299 FALSE FALSE FALSE 51.2
#> tRNAscan_potential.pseudogene tRNAscan_intron tRNAscan_hmm.score
#> <logical> <logical> <numeric>
#> 1 FALSE TRUE 37.9
#> 2 FALSE FALSE 53.4
#> 3 FALSE TRUE 27.0
#> 4 FALSE FALSE 49.7
#> 5 FALSE FALSE 45.3
#> ... ... ... ...
#> 295 FALSE FALSE NA
#> 296 FALSE FALSE NA
#> 297 FALSE FALSE NA
#> 298 FALSE FALSE NA
#> 299 FALSE FALSE 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
#> ... ... ...
#> 295 NA NA
#> 296 NA NA
#> 297 NA NA
#> 298 NA NA
#> 299 NA NA