predictDistance: Return list of calculated RNA distance

Description Usage Arguments Value Author(s) References Examples

View source: R/Prediction.R

Description

Perform RNA distance calculation based on imported file or input of RNA orginal sequence and alternative sequence. The RNA distance calculation is based on the RNAdistance command line algorithm by Walter Fontana, Ivo L Hofacker, Peter F Stadler. RNA distance calculation is based on -XF parameter, which indicates single alignment among each comparisons. MacOS or Unix user can ignore executable.path, when RNADistance is already installed in the system tools.

Usage

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predictDistance(
  executable.path = "",
  name = c(),
  struct.ori = c(),
  struct.alt = c(),
  method = "gsc"
)

Arguments

executable.path

The path referred to RNADistance executable (.../RNADistance) used by program

name

List consisted with name of the RNA sequence in seq

struct.ori

List consisted with RNA orginal sequence

struct.alt

List consisted with RNA alternative sequence

method

Options to use "RNADis" (RNADistance) or "gsc" gscVisualizer package for RNAdistance calculation, default value is "gsc"

Value

Returns a list of RNA distance, ordered according to the input name sequence

Author(s)

Sijie Xu, sijie.xu@mail.utoronto.ca

References

Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. ViennaRNA Package 2.0 Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26

Examples

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dot <- predictDistance(name = c("hsa-let-7b", "hsa-let-7a-2")
, struct.ori = c("(((((.(((((((((((((((((((((((.....))).)))).))).....))))))))))))))))))",
"(((((.(((((((((((((((((((((((.....))).)))).))).....))))))))))))))))))")
, struct.alt = c("(((((.((((((((((((..(((((((((.....)))))).).....))...)))))))))))))))))",
"(((((.((((((((.((((((((((((((.....)))))).).))).....))))))))))).))))))"))

JackXu2333/rseAnalysis documentation built on Dec. 31, 2020, 1:10 p.m.