LearnNonCoding {DECIPHER} | R Documentation |
Learns a compact representation of patterns representing a set of non-coding RNAs belonging to the same family.
LearnNonCoding(myXStringSet, threshold = 0.3, weight = NA, maxLoopLength = 500, maxPatterns = 20, scoreDependence = FALSE, structure = NULL, processors = 1)
myXStringSet |
A |
threshold |
Numeric specifying the minimum relative frequency of patterns to consider during learning. |
weight |
Either a numeric vector of weights for each sequence, a single number implying equal weights, or |
maxLoopLength |
Numeric giving the maximum length of conserved hairpin loops to consider. |
maxPatterns |
A numeric vector of length two specifying the maximum number of motifs and hairpins, respectively, or a single numeric giving the maximum for each. |
scoreDependence |
Logical determining whether to record a log-odds score for dependencies between patterns. The default ( |
structure |
Either a character string providing the consensus secondary structure in dot bracket notation, a matrix of paired positions in the first two columns, or |
processors |
The number of processors to use, or |
Non-coding RNAs belonging to the same family typically have conserved sequence motifs, secondary structure elements, and k-mer frequencies that can be used to identify members of the family. LearnNonCoding
identifies these conserved patterns and determines which are best for identifying the non-coding RNA relative to a random sequence background. Sequence motifs and hairpins are defined relative to their distance from the start or end of the non-coding RNA, allowing the precise and rapid identification of the boundaries of any matches to the non-coding RNA in a genome.
An object of class NonCoding
.
Erik Wright eswright@pitt.edu
FindNonCoding
, NonCoding-class
# import a family of non-coding RNAs fas_path <- system.file("extdata", "IhtA.fas", package="DECIPHER") rna <- readRNAStringSet(fas_path) rna # align the sequences RNA <- AlignSeqs(rna) RNA y <- LearnNonCoding(RNA) y y[["motifs"]] y[["hairpins"]] head(y[["kmers"]])