read.genepix {phyloarray}R Documentation

Reading genepix-file

Description

Read a genepix-file ('.gpr') and stores result in a list containing 'header' and 'data'.

Usage

  read.genepix2(file, temperature=42, buffer=data.frame(na=0.97, f=35))

Arguments

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).

Value

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.

Note

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.

Author(s)

Kurt Sys (kurt.sys@advalvas.be)

References

See Also

Scandataraw Phylodata

init.data

Examples

  # 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

[Package Contents]