mzML2diskFrame: Convert mz data to disk.frame

In pmbrophy/mzDataTable: Import and convert raw mass spectrometry data formats

Description

Convert .mzML file to disk.frame using mzR, data.table, and disk.frame

Usage

mzML2diskFrame(path, diskFramePath, scans = NULL, chunkSize = 100)

Arguments

path	path to the mzML file
diskFramePath	path and fileName.df specifying write location of .df directory
scans	Optional parameter. Provide a numeric vector to import select scans and write to a data.frame. If not provided, the whole file is converted. Default is NULL.
chunkSize	number of scans to be extracted and written to the disk.frame at a time. Useful for breaking up large data files and converting to disk.frame. Default is 100. If NULL, imports all scans in single operation and you will probably run out of memory.

Value

Returns a disk.frame reference object.

Examples

## Not run: 
#read .mzML file from system path and write to disk.frame
#100 scans (default) at a time
mzML2diskFrame(path = path_2_mzML,
               diskFramePath = "dfPath.df")

#read scans 100-200 from .mzML file specified by a system path
#and write to disk.frame 20 scans at a time
mzML2diskFrame(path = path_2_mzML,
               diskFramePath = "dfPath.df",
               scans = c(100:200),
               chunkSize = 20)

## End(Not run)

pmbrophy/mzDataTable documentation built on June 6, 2020, 7:43 a.m.