NonCoding {DECIPHER} | R Documentation

## NonCoding Objects and Methods

### Description

Non-coding RNAs can be represented by their conserved sequence motifs, secondary structure, and k-mer frequencies. Class `NonCoding` provides objects and functions for representing non-coding RNAs.

### Usage

    ## S3 method for class 'NonCoding'
    print(x, ...)

### Arguments

`x` | An object of class `NonCoding`.
`...` | Other optional parameters.

### Details

Objects of class `NonCoding` are stored as lists containing a compact representation of a family of non-coding RNAs. The first list component is a matrix of sequence motifs that identify the non-coding RNAs, the second is a matrix of hairpin loops that are conserved across the family, the third is a list of k-mer frequencies derived from representative sequences, and the fourth is a vector of log-odds scores for sequence lengths. An optional fifth list component denotes the log-odds scores for dependencies among patterns. Patterns are defined by their distance to either end of the non-coding RNA, which helps to identify the boundaries of the non-coding RNA in a genome.

### Author(s)

Erik Wright eswright@pitt.edu

### See Also

`LearnNonCoding`, `FindNonCoding`

### Examples

    data(NonCodingRNA_Bacteria)
    x <- NonCodingRNA_Bacteria
    print(x)
    class(x)
    attributes(x[[1]])
    x[[1]] # the first non-coding RNA
    x[[1]][["motifs"]] # sequence motifs
    x[[1]][["hairpins"]] # hairpin loops
    head(x[[1]][["kmers"]]) # k-mer frequencies

[Package DECIPHER version 2.22.0 Index]