Nothing
ConsensusSequence <- function(myXStringSet,
threshold=0.05,
ambiguity=TRUE,
noConsensusChar="+",
minInformation=1 - threshold,
ignoreNonBases=FALSE,
includeTerminalGaps=FALSE) {
# error checking
if (!is(myXStringSet, "DNAStringSet") && !is(myXStringSet, "RNAStringSet") && !is(myXStringSet, "AAStringSet"))
stop("myXStringSet must be an AAStringSet, DNAStringSet, or RNAStringSet.")
if (!is.logical(ambiguity))
stop("ambiguity must be a logical.")
if (!is.numeric(threshold))
stop("threshold must be a numeric.")
if (threshold >= 1)
stop("threshold must be less than one.")
if (threshold < 0)
stop("threshold cannot be negative.")
if (!is.numeric(minInformation))
stop("minInformation must be a numeric.")
if (minInformation > 1)
stop("minInformation cannot be greater than one.")
if (minInformation <= 0)
stop("minInformation must be greater than zero.")
if (is(myXStringSet, "DNAStringSet") && is.na(pmatch(noConsensusChar, DNA_ALPHABET)))
stop("noConsensusChar must be a character in the DNA_ALPHABET.")
if (is(myXStringSet, "RNAStringSet") && is.na(pmatch(noConsensusChar, RNA_ALPHABET)))
stop("noConsensusChar must be a character in the RNA_ALPHABET.")
if (is(myXStringSet, "AAStringSet") && is.na(pmatch(noConsensusChar, AA_ALPHABET)))
stop("noConsensusChar must be a character in the AA_ALPHABET.")
if (!is.logical(ignoreNonBases))
stop("ignoreNonBases must be a logical.")
if (is(myXStringSet, "AAStringSet")) {
seq <- .Call("consensusSequenceAA",
myXStringSet,
threshold,
ambiguity,
minInformation,
ignoreNonBases,
includeTerminalGaps,
PACKAGE="DECIPHER")
} else { # DNAStringSet or RNAStringSet
seq <- .Call("consensusSequence",
myXStringSet,
threshold,
ambiguity,
minInformation,
ignoreNonBases,
includeTerminalGaps,
PACKAGE="DECIPHER")
if (is(myXStringSet, "RNAStringSet"))
seq[1] <- gsub("T",
"U",
seq[1],
fixed=TRUE)
}
seq[1] <- gsub("?",
noConsensusChar,
seq[1],
fixed=TRUE)
if (is(myXStringSet, "DNAStringSet")) {
consensusSeq <- DNAStringSet(seq[1])
} else if (is(myXStringSet, "RNAStringSet")) {
consensusSeq <- RNAStringSet(seq[1])
} else { # AAStringSet
consensusSeq <- AAStringSet(seq[1])
}
return(consensusSeq)
}
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