gettRNABasePairing {tRNA}R Documentation

Accessing Dot Bracket annotation of tRNAs

Description

gettRNABasePairing converts the dot bracket annotation into a DotBracketDataFrame. Base pairing is indicated by cosrresponding numbers in the forward and reverse columns. For more detail have a look at getBasePairing.

gettRNALoopIDs converts the dot bracket annotation into a LoopIDList. For more details have a look at getLoopIDList.

Usage

gettRNABasePairing(x, with.nucleotides = FALSE)

gettRNALoopIDs(x)

## S4 method for signature 'GRanges'
gettRNABasePairing(x, with.nucleotides = FALSE)

## S4 method for signature 'GRanges'
gettRNALoopIDs(x)

Arguments

x

a GRanges object created by import.tRNAscanAsGRanges or GRanges with equivalent information. The tRNA_str and tRNA_seq columns will be used to construct a StructuredXStringSet and used for input into getBasePairing.

with.nucleotides

a single logical value: should the nucleotides be saved alongside the base pairing information in the 'base' column?

Value

gettRNABasePairing: The result is a DotBracketDataFrame with following columns: pos, forward, reverse, character and base. If a position is unpaired, forward and reverse will be 0, otherwise it will match the base paired positions.

gettRNALoopIDs: return a list of list of loop ids.

Examples

data("gr", package = "tRNA")
gettRNABasePairing(gr[1])
gettRNALoopIDs(gr[1])
[Package tRNA version 1.5.2 Index]