Nothing
limmaAnalyze <- function(UTR3eset, design, contrast.matrix, coef=1, robust=FALSE, ...){
if(missing(design)||missing(contrast.matrix)){
stop("desing and contrast.matrix is required.")
}
if(!is(design, "matrix")){
stop("design must be an design matrix")
}
if(!is(contrast.matrix, "matrix")){
stop("contrast.matrix must be an object of matrix")
}
if(!is(UTR3eset, "UTR3eSet")){
stop("UTR3eset must be an object of UTR3eSet")
}
short <- UTR3eset@short
long <- UTR3eset@long
if(!identical(rownames(short), rownames(long))){
stop("the rownames are not identical for short form and long form")
}
txid <- rep(rownames(short), 2)
formid <- c(paste(rownames(short), "short", sep=":"),
paste(rownames(long), "long", sep=":"))
y <- rbind(short, long)
rownames(y) <- formid
lib.size <- colSums(y)
y <- log2(y+0.001)
y <- normalizeBetweenArrays(y)
fit <- lmFit(y, design, ...)
fit <- contrasts.fit(fit, contrast.matrix)
ex <- diffSplice(fit, geneid=txid, exonid=formid,
robust=robust, verbose=FALSE)
ts <- topSplice(ex, coef=coef, test="simes", number=nrow(ex))
p <- ts[match(rownames(short), ts$GeneID), "P.Value"]
BH <- ts[match(rownames(short), ts$GeneID), "FDR"]
out <- cbind(P.Value=p, adj.P.Val=BH)
rownames(out) <- rownames(short)
out
}
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