dbcypherGenXML2Bin: Convert Cyphergen XML files into binary files

In zeehio/msProcess: Protein Mass Spectra Processing

Description

Convert one or a set of Cyphergen XML files into binary files to be imported into SQLite database.

Usage

cypherGenXML2Bin(name, pattern, path, mz, tof = FALSE, maxRows = 10000, 
	append = TRUE, verbose=TRUE, ...)
cypherGenXMList2BinBlocks(x, pattern, tof = FALSE, maxRows = 10000, 
	maxCols = NULL, path = ".", category = NULL, verbose = 1, ...)

Arguments

name	A character string specifying the name of a xml file.
pattern	A character string to specify the common prefix for a series of binary files.
path	A character to specify the name of input directory.
mz	A numeric vector specifying mz peaks to be used.
maxRows	An integer defining the maximum number of rows in a binary file.
tof	A logical indicating whether TOF data or the processed data should be read.
append	A logical. If FALSE, then existing files will be overwritten. Otherwise, data will be appended onto the existing file.
x	A vector of characters specifying a set of XML files to be imported.
maxCols	An integer defining the maximum number of columns in a binary file, or NULL, in which case all xml files will be put into one sqliteTable.
category	A data.frame object containing categorical information.
verbose	A logical or a non-negative integer value to control whether or not to print out extra messages during processing. The larger the value, the more information is printed out.
...	Additional optional arguments.

Details

cypherGenXML2Bin converts a single Cyphergen XML file into a series of binary files via function writeBinBlocks. Each file contains at most maxRows mz peaks. Currently we assume calibration has been made by Cyphergen mass spectrometer. We might support customized input of a, b, t0, u in the future.

cypherGenXMList2BinBlocks is a batch version of cypherGenXML2Bin. It converts a list of xml files into a list of binary files. Each binary file contains at most maxRows rows and maxCols columns. If provided, category will be used as group factor to partition XML files into groups, and each binary file contains XML files within the same group.

mz provides a calibration standard to make all mass spectra sharing the same set of mass-charge ratio peaks.

maxRows is used as input to mxRow in function writeBinBlocks.

Value

cypherGenXML2Bin returns NULL.

cypherGenXMList2BinBlocks returns a list containing the following items:

sampleTable	A data frame that contains table topology.
categoryTable	A data frame that contains categorical information.

Author(s)

Y. Alex Chen <[e-mail]>

See Also

readBinMatrix, writeBinBlocks, importBin2Sqlite

zeehio/msProcess documentation built on May 4, 2019, 10:15 p.m.