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 2.21.0 Index]