[Seqinr-commits] r1531 - pkg/man

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2009-01-22 20:02:45 +0100 (Thu, 22 Jan 2009)
New Revision: 1531

Added:
   pkg/man/gs500liz.Rd
Log:
new dataset GS500LIZ

Added: pkg/man/gs500liz.Rd
===================================================================
--- pkg/man/gs500liz.Rd	                        (rev 0)
+++ pkg/man/gs500liz.Rd	2009-01-22 19:02:45 UTC (rev 1531)
@@ -0,0 +1,43 @@
+\name{gs500liz}
+\alias{gs500liz}
+\docType{data}
+\title{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.
+  \describe{
+    \item{liz}{a vector of 16 values for the fragment sizes in bp.}
+    \item{mask1}{a vector of 16 logicals to remove fragments whose
+  migration may be anomalous (250 and 340 bp).}
+    \item{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)
+}