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