FindNonCoding {DECIPHER} | R Documentation

## Find Non-Coding RNAs in a Genome

### Description

Searches for conserved patterns representing a family of non-coding RNAs. Returns the start and end boundaries of potential matches along with their log-odds score.

### Usage

    FindNonCoding(x,
                  myXStringSet,
                  minScore = 16,
                  allScores = FALSE,
                  processors = 1,
                  verbose = TRUE)

### Arguments

`x` | A `NonCoding` object or a list of `NonCoding` objects for searching.
`myXStringSet` | A `DNAStringSet` or `RNAStringSet` object of unaligned sequences, typically representing a genome.
`minScore` | Numeric giving the minimum log-odds score of matches to `x` in `myXStringSet` to report, or a vector of numerics specifying the minimum score per `NonCoding` object in `x`. The maximum false discovery rate is approximately `exp(-minScore)` per nucleotide per object in `x`.
`allScores` | Logical specifying whether all matches should be returned (`TRUE`) or only the top matches when there are multiple matches in the same region.
`processors` | The number of processors to use, or `NULL` to automatically detect and use all available processors.
`verbose` | Logical indicating whether to display progress.

### Details

Non-coding RNAs are identified by the location of representative sequence patterns relative to the beginning and end of the non-coding RNA. Potential matches to each `NonCoding` object in `x` are scored based on their log-odds relative to a background that is derived from the input sequence (`myXStringSet`). Matches of at least `minScore` are returned as a `Genes` object with the `"Gene"` column set to the negative index of the list element of `x` that was identified.

### Value

An object of class `Genes`.

### Author(s)

Erik Wright eswright@pitt.edu

### See Also

`LearnNonCoding`, `NonCoding-class`, `ExtractGenes`, `Genes-class`, `WriteGenes`

### Examples

    data(NonCodingRNA_Bacteria)
    x <- NonCodingRNA_Bacteria
    names(x)

    # import a test genome
    fas <- system.file("extdata",
    	"Chlamydia_trachomatis_NC_000117.fas.gz",
    	package="DECIPHER")
    genome <- readDNAStringSet(fas)

    z <- FindNonCoding(x, genome)
    z

    annotations <- attr(z, "annotations")
    m <- match(z[, "Gene"], annotations)
    sort(table(names(annotations)[m]))

    genes <- ExtractGenes(z, genome, type="RNAStringSet")
    genes

[Package DECIPHER version 2.22.0 Index]