FindNonCoding {DECIPHER} | R Documentation |
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.
FindNonCoding(x, myXStringSet, minScore = 16, allScores = FALSE, processors = 1, verbose = TRUE)
x |
A |
myXStringSet |
A |
minScore |
Numeric giving the minimum log-odds score of matches to |
allScores |
Logical specifying whether all matches should be returned ( |
processors |
The number of processors to use, or |
verbose |
Logical indicating whether to display progress. |
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.
An object of class Genes
.
Erik Wright eswright@pitt.edu
LearnNonCoding
, NonCoding-class
, ExtractGenes
, Genes-class
, WriteGenes
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