Nothing
###################################################################
## This creates object of class igraph.
write.qtlnet <- function(x,
filename,
edges = get.averaged.net(x, ...),
loci.list = loci.qtlnet(x, ...),
include.qtl=TRUE,
est.list = est.qtlnet(x, ...),
include.est=TRUE,
digits = 3,
col.names = TRUE,
...)
{
out <- cbind(cause = as.character(edges[[1]]),
type = rep("Causal", nrow(edges)),
effect = as.character(edges[[2]]))
out.width <- edges[[3]]
if(!is.null(loci.list) & include.qtl) {
qtl <- unlist(loci.list)
loci <- cbind(cause = qtl,
type = rep("QTL", length(qtl)),
effect = rep(names(loci.list), sapply(loci.list, length)))
loci.width <- rep(1, nrow(loci))
out <- rbind(out, loci)
out.width <- c(out.width, loci.width)
}
out <- as.data.frame(out, stringsAsFactors = TRUE)
out$width <- round(out.width, digits)
if(include.est) {
## Need to figure out how to add estimates of edge coef.
tmp <- rep(NA, nrow(out))
for(effect in levels(out$effect)) {
ii <- out$effect == effect
if(any(ii)) {
m <- match(as.character(out$cause)[ii], names(est.list[[effect]]),
nomatch = 0)
tmp[ii][m > 0] <- est.list[[effect]][m]
}
}
out$coef <- tmp
}
utils::write.table(out, file = filename, quote = FALSE,
col.names = col.names, row.names = FALSE)
invisible(out)
}
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