Enable usage of old xcms code

This function allows to enable the usage of old, partially deprecated code from xcms by setting a corresponding global option. See details for functions affected.

Usage

useOriginalCode(x)

Arguments

x

logical(1) to specify whether or not original old code should be used in corresponding functions. If not provided the function simply returns the value of the global option.

Value

logical(1) indicating whether old code is being used.

Details

The functions/methods that are affected by this option are:

• do_findChromPeaks_matchedFilter: use the original code that iteratively creates a subset of the binned (profile) matrix. This is helpful for computers with limited memory or matchedFilter settings with a very small bin size.

• getPeaks

Note

For parallel processing using the SOCKS method (e.g. by SnowParam() on Windows computers) this option might not be passed to the individual R processes performing the calculations. In such cases it is suggested to specify the option manually and system-wide by adding the line options(XCMSuseOriginalCode = TRUE) in a file called .Rprofile in the folder in which new R processes are started (usually the user's home directory; to ensure that the option is correctly read add a new line to the file too). See also Startup from the base R documentation on how to specify system-wide options for R.

Usage of old code is strongly dicouraged. This function is thought to be used mainly in the transition phase from xcms to xcms version 3.

Author

Johannes Rainer