Nothing
table2xs <- function(pn, ...) {
UseMethod("table2xs")
}
table2xs.BasicGOProfile <- function(pn, qm=NULL, pqn0=NULL, goIds=F)
{
freq.col <- 3
namsPn <- rownames(pn)
n <- ngenes(pn)
if (!is.null(qm)) {
namsQm <- rownames(qm)
m <- ngenes(qm)
}
else namsQm <- NULL
if (!is.null(pqn0)) {
namsPQn0 <- rownames(pqn0)
n0 <- ngenes(pqn0)
if (!is.null(qm)) {
if (!all((namsPQn0 %in% namsQm)))
stop("All GO nodes in 'pqn0' should be also present in 'qm'")
}
else m <- n0
if (!all((namsPQn0 %in% namsPn)))
stop("All GO nodes in 'pqn0' should be also present in 'pn'")
commn <- namsPn %in% namsPQn0
pn[commn,freq.col] <- pn[commn,freq.col] - pqn0[namsPn[commn],freq.col]
n <- n - n0
}
else namsPQn0 <- NULL
nams <- unique(c(namsPn, namsQm, namsPQn0))
tabFreqs <- matrix(0, nrow = length(nams), ncol=2)
rownames(tabFreqs) <- nams
tabFreqs[,1][aux] <- pn[nams[aux <- nams %in% namsPn],freq.col]
if (!is.null(qm))
tabFreqs[,2][aux] <- qm[nams[aux <- nams %in% namsQm],freq.col]
else
tabFreqs[,2][aux] <- pqn0[nams[aux <- nams %in% namsPQn0],freq.col]
tabFreqs <- tabFreqs[tabFreqs[,1]|tabFreqs[,2],]
attr(tabFreqs,"ngenes") <- c(n,m)
if (goIds) {
goIdsTable <- unique(c(as.character(pn[rownames(pn),"GOID"]), as.character(qm[rownames(qm),"GOID"])))
names(goIdsTable) <- unique(c(rownames(pn), rownames(qm)))
rownames(tabFreqs) <- goIdsTable[rownames(tabFreqs)]
}
return(tabFreqs)
}
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