Description Usage Arguments Details Value Author(s) See Also
Convert one or a set of Cyphergen XML files into binary files to be imported into SQLite database.
1 2 3 4 |
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 |
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 |
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
|
category |
A |
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. |
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
.
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. |
Y. Alex Chen <ychen@insightful.com>
readBinMatrix, writeBinBlocks, importBin2Sqlite
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