gs500liz: GS500LIZ size standards

In seqinr: Biological Sequences Retrieval and Analysis

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)

Format

A list with 3 components.

liz

a vector of 16 values for the fragment sizes in bp.

mask1

a vector of 16 logicals to remove fragments whose migration may be anomalous (250 and 340 bp).

mask2

a vector of 16 logicals to remove extreme fragments (35, 50, 490, 500 bp) so that the resulting fragments are in the 75-450 bp range.

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)

seqinr documentation built on March 31, 2023, 3:05 p.m.