useOriginalCode {xcms} | R Documentation

## Enable usage of old xcms code

### Description

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.

### 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

### Value

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

### 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(s)

Johannes Rainer

[Package xcms version 3.10.2 Index]