Nothing
### Typical 'prior.params' vector: c(A=0.25, C=0.25, G=0.25, T=0.25)
### This is taken from Biostrings package matchPWM.R.
### Just to get rid of the node during the build.
DNA_BASES <- c("A", "C", "G", "T")
normargPriorParams <- function(prior.params)
{
if (!is.numeric(prior.params))
stop("'prior.params' must be a numeric vector")
if (length(prior.params) != length(DNA_BASES) ||
!setequal(names(prior.params), DNA_BASES))
stop("'prior.params' elements must be named A, C, G and T")
## Re-order the elements.
prior.params <- prior.params[DNA_BASES]
if (any(is.na(prior.params)) || any(prior.params < 0))
stop("'prior.params' contains NAs and/or negative values")
prior.params
}
normargMat = function(x){
if (is.null(rownames(x)))
stop("invalid Matrix 'mat': no row names")
if (!all(DNA_BASES %in% rownames(x)))
stop("invalid Matrix 'mat': row names must contain A, C, G and T")
if (any(duplicated(rownames(x))))
stop("invalid Matrix 'mat': duplicated row names")
if (ncol(x) == 0L)
stop("invalid Matrix 'mat': no columns")
if (any(is.na(x)) || any(x < 0L))
stop("invalid Matrix 'mat': values cannot be NA or negative")
if (any(x[!(rownames(x) %in% DNA_BASES), ] != 0L))
stop("invalid Matrix 'mat': IUPAC ambiguity letters are represented")
x <- x[DNA_BASES, , drop = FALSE]
x
}
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