| read.genepix {phyloarray} | R Documentation |
Read a genepix-file ('.gpr') and stores result in a list containing 'header' and 'data'.
read.genepix2(file, temperature=42, buffer=data.frame(na=0.97, f=35))
file |
The name of the file to be read. The extension should be given. |
temperature |
The temperature of hybridization (or washing) step. Since there's a focus on melting curves, this is important and the value given here will be added to the header. |
buffer |
Buffer contents used during hybridization (or washing). This is not used anywhere yet, but it might e.g. to calculate the theoretical melting/annealing temperature based on the sequence and the buffer content. 'na' is the salt (Na)–content and 'f' the formamide concentration (in percent). |
The function returns a list containing:
Header |
A list with the header fields of the .gpr-file, with
additional information concerning the hybridization temperature and
buffer contents (given as arguments to the function. |
Data |
A data matrix with the data in a .gpr-file. This
includes median and mean values for fore- and background, as well as
probe ID's, standard deviations, X and Y values etc. |
Since there is a function read.genepix in sma, this function has
been called read.genepix2. It must be noted that for new versions of
genepix, the function in the sma-package doesn't work (since more
columns are added). This function works for both, but I have really no
idea how the future will be... Anyway I tried to make it as general as
possible.
Data from other image processing software (e.g. Spot) may be imported
using the package sma. In that case, one should know the names
of the fields of the red/green signals etc.
Kurt Sys (kurt.sys@advalvas.be)
# There are this-is-escaped-codenormal-bracket36bracket-normal-files in the data-section of this package
#
# scan1 <- read.genepix2("<file_scan.at.22degrees>", temperature=22)
# ...
# scan3 <- read.genepix2("<file_scan.at.58degrees>", temperature=58)
#
#
# or, e.g.:
#
# scan <- 1
# for (t in c(22+0:2*18)) normal-bracket37bracket-normal
# assign(paste("scan", slide, sep=""),
# read.genepix2(paste("wash", t, ".gpr", sep=""), temperature=t))
# scan <- scan+1
# normal-bracket37bracket-normal