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

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