NonCoding {DECIPHER} | R Documentation |
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.
## S3 method for class 'NonCoding' print(x, ...)
x |
An object of class |
... |
Other optional parameters. |
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.
Erik Wright eswright@pitt.edu
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