r2easyR.pk_finder: Identifies non-nested base pairs (pseudoknots) from an RNA...
In JPSieg/R2easyR: Facilitates Mapping Experimental RNA Reactivity Data to Secondary Structures Drawn with R2R
View source: R/r2easyR.pk_finder.R
r2easyR.pk_finder R Documentation
Identifies non-nested base pairs (pseudoknots) from an RNA secondary structure specified
by a connectivity table (.ct) formatted data frame.
Description
Capable of identifying multiple pseudoknots and pseudoknots within pseudoknots.
Returns a modified data frame with pseudoknotted base pairs deleted and a list
of vectors of the pseudoknot base pairs. Pseudoknots can be passed to the r2easyR.pknot_drawer.
Pseudoknots are troublesome for structure drawing programs because their non-nested nature
fools the drawing program into pairing the incorrect bases.
Usage
r2easyR.pk_finder(ctdata_frame)
Arguments
ctdata_frame
A data frame made by reading a .ct file into R with read.ct
Value
A list of two elements, the first is the modified data frame with the pseudoknots deleted from the dotbracket column and the second is a list of vectors identifying pseudonotted bases.
JPSieg/R2easyR documentation built on March 2, 2024, 8:42 a.m.
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View source: R/r2easyR.pk_finder.R
| r2easyR.pk_finder | R Documentation |
Identifies non-nested base pairs (pseudoknots) from an RNA secondary structure specified by a connectivity table (.ct) formatted data frame.
Description
Capable of identifying multiple pseudoknots and pseudoknots within pseudoknots. Returns a modified data frame with pseudoknotted base pairs deleted and a list of vectors of the pseudoknot base pairs. Pseudoknots can be passed to the r2easyR.pknot_drawer. Pseudoknots are troublesome for structure drawing programs because their non-nested nature fools the drawing program into pairing the incorrect bases.
Usage
r2easyR.pk_finder(ctdata_frame)
Arguments
ctdata_frame |
A data frame made by reading a .ct file into R with read.ct |
Value
A list of two elements, the first is the modified data frame with the pseudoknots deleted from the dotbracket column and the second is a list of vectors identifying pseudonotted bases.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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