hasTStem {tRNA} | R Documentation |
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 signature 'GRanges' hasTStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA) ## S4 method for signature 'GRanges' hasDStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA) ## S4 method for signature 'GRanges' hasAcceptorStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA) ## S4 method for signature 'GRanges' hasAnticodonStem(x, length = NA, unpaired = NA, mismatches = NA, bulged = NA) ## S4 method for signature 'GRanges' hasTloop(x, length = NA) ## S4 method for signature 'GRanges' hasDloop(x, length = NA) ## S4 method for signature 'GRanges' hasAnticodonLoop(x, length = NA) ## S4 method for signature 'GRanges' hasVariableLoop(x, length = NA, paired = NA, mismatches = NA, bulged = NA)
x |
a GRanges object from a tRNAscan import or with equivalent information |
length |
the length as integer |
unpaired |
logical: has unpaired nucleotides |
mismatches |
logical: has mismatched nucleotides |
bulged |
logical: has mismatched nucleotides of different length creating a bulge |
paired |
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) gr[hasTStem(gr, length = 5, mismatches = TRUE)] gr[hasDStem(gr, unpaired = FALSE) & hasDStem(gr, mismatches = FALSE)]