predictDistance: Return list of calculated RNA distance

In JackXu2333/dseAnalysis: Correlation analysis of RNA secondary structure mutation and differential expression

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

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, [e-mail]

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

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

JackXu2333/dseAnalysis documentation built on Dec. 31, 2020, 1:09 p.m.