seqinr (version 3.1-2)

gs500liz: GS500LIZ size standards

Description

GS500LIZ is an internal size standard often used in capillary electrophoresis. It contains 16 fragments ranging in size from 35 to 500 bp. Note that they are not all used for calibration : fragments at 250 and 340 bp may migrate anomalously (most likey because of secondary structure formation).

Usage

data(gs500liz)

Examples

data(gs500liz)
op <- par(no.readonly = TRUE)
par(lend = "butt", mar = c(5,0,4,0)+0.1)
x <- gs500liz$liz
n <- length(x)
y <- rep(1, n)
plot(x, y, type = "h", yaxt = "n", xlab = "Fragment size [bp]",
  main = "GS500LIZ size standard", lwd = 2)
x1 <- x[!gs500liz$mask1]
segments(x1, 0, x1, 1, col = "red", lwd = 2)
x2 <- x[!gs500liz$mask2]
segments(x2, 0, x2, 1, col = "blue", lwd = 2)
col <- rep("black", n)
col[!gs500liz$mask1] <- "red"
col[!gs500liz$mask2] <- "blue"
text(x,1.05,paste(x, "bp"), srt = 90, col = col)
legend("top", inset = 0.1, legend = c("regular", "imprecise (mask1)", "extreme (mask2)"),
  lwd = 2, col = c("black","red","blue"))
par(op)