RNAplfoldR: Estimate nucleotide resolution transcript accessibilty for a...
In Santaris/seqtools: Tools for oligonucleotide-centric sequence analysis
Description
This function is the R version of RNAplfold from the ViennaRNA package (Tafer et al., 2008). It
evaluates accessibility (probability of being unpaired) for a transcript. The VienneRNA
package needs to be installed (version 2.0.7 from http://www.tbi.univie.ac.at/~ronny/RNA/vrna2_source.html).
Usage
1
RNAplfoldR(seq.char, L.in = 40, W.in = 80, u.in = 16)
Arguments
seq.char
a character vector with the nucleotide sequence
L.in
allow only pairs (i,j) with j-i <= L.in
W.in
average pair probabilities over windows of size W.in.
u.in
compute the mean probability that regions of length 1 to u.in are unpaired.
Santaris/seqtools documentation built on May 9, 2019, 12:44 p.m.
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Description
This function is the R version of RNAplfold from the ViennaRNA package (Tafer et al., 2008). It evaluates accessibility (probability of being unpaired) for a transcript. The VienneRNA package needs to be installed (version 2.0.7 from http://www.tbi.univie.ac.at/~ronny/RNA/vrna2_source.html).
Usage
1 | RNAplfoldR(seq.char, L.in = 40, W.in = 80, u.in = 16)
|
Arguments
seq.char |
a character vector with the nucleotide sequence |
L.in |
allow only pairs (i,j) with j-i <= L.in |
W.in |
average pair probabilities over windows of size W.in. |
u.in |
compute the mean probability that regions of length 1 to u.in are unpaired. |
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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