?Sweave
Stangle("qtlhot.Rnw")
q()
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help.start()
Making packages.html  ... done
!ls
system("ls")
Sweave("qtlhot.Rnw")
Sweave("qtlhot.Rnw")
Sweave("qtlhot.Rnw")
system("pdflatex qtlhot; pdflatex qtlhot")
par(mar = c(4.1,4.1,0.1,4.1))
plot(out2, lodcolumn = 5, ylab = "counts", cex.lab = 1.5, cex.axis = 1.5)
plot(hot.scan2, lodcolumn = 2, add = TRUE, col = "red")
## Add right axis with 
quant <- attr(hot.scan2, "quant")
tmp <- seq(along = quant)
axis(4, at = tmp, label = round(quant[tmp], 2), las = 1, cex = 0.5)

mtext
mtext("sliding LOD thresholds",3)
mtext("sliding LOD thresholds",4)
mtext("sliding LOD thresholds",4, 1, cex=2)
mtext("sliding LOD thresholds",4, 1, cex=1.5)
Sweave("qtlhot.Rnw")
objects()
plot(out1, lodcolumn = 5, ylab = "counts", cex.lab = 1.5, cex.axis = 1.5)
plot(hot.scan1, lodcolumn = 2, add = TRUE, col = "red")

hot.scan1 <- qtlhot.scan(cross1, scan1, NL.N.1$max.lod.quant, lod.thrs, probs = seq(.01, .1, by = .01), level = 0.05)

qtlhot.scan
quant.slide( NL.N.1$max.lod.quant, lod.thrs, probs = seq(.01, .1, by = .01), level = 0.05)
qtlhot:::quant.slide( NL.N.1$max.lod.quant, lod.thrs, probs = seq(.01, .1, by = .01), level = 0.05)
debug(qtlhot:::quant.slide)
qtlhot:::quant.slide( NL.N.1$max.lod.quant, lod.thrs, probs = seq(.01, .1, by = .01), level = 0.05)
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max.quant
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quant.level
quant
Q
undebug(qtlhot:::quant.slide)
Sweave("qtlhot.Rnw")
system("pdflatex qtlhot; pdflatex qtlhot")
q()
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