msc.project.run {caMassClass} | R Documentation |
Read and preprocess protein mass spectra (SELDI) files where files could contain multiple copies of spectra taken from the same sample, or spectra from multiple experiments performed on the same sample.
msc.project.run(ProjectFile, directory.out=NULL, verbose = TRUE, ...)
ProjectFile |
path and name of text file in Excel's CSV format which is used to store information about a batch of Mass Spectra data files. See details. |
directory.out |
Optional character vector with name of directory where
output files will be saved. Use "/" slashes
in directory name. By default the directory containing ProjectFile
and all Mass Spectra files is used, and this argument is provided in case
that directory is read-only and user have to choose a different directory. |
verbose |
boolean flag turns debugging printouts on. |
... |
parameters to be passed to msc.preprocess.run |
High level processing of protein mass spectra (SELDI) data.
msc.project.read
supports projects with multiple
sets of spectra taken under different experimental condition. Those sets
will be called batches. With that in mind, following steps
are performed:
msc.project.read(ProjectFile, directory)
is called
which reads and saves different batches of mass spectra (SELDI) data into
separate files.
List of those files is saved in temporary "RInputFiles.csv" file.
In future calls to msc.project.run
, if above file exist than
msc.project.read
is not called again.
load
ed and preprocessed by
calls to msc.preprocess.run
. All the required parameters
have to be passed through "..." mechanism.
rbind
ed
X |
Spectrum data either in matrix format [nFeatures x
nSamples]. Row names
(rownames(X) store M/Z mass of each row merged with batch name |
SampleLabels |
Class label for each sample as read from
msc.project.read |
SameSample |
array of the same length as number of columns in X
indicating samples that are multiple copies that came from the same
physical sample, and should be the same, if not for noise. |
mxXML |
Experiment information in mzXML file format. Included only if
input data was read from mzXML files, and NULL otherwise. |
Jarek Tuszynski (SAIC) jaroslaw.w.tuszynski@saic.com
msc.project.read
, msc.preprocess.run
directory = system.file("Test", package = "caMassClass") ProjectFile = file.path(directory,"InputFiles.csv") Data = msc.project.run(ProjectFile, '.', baseline.removal=0, mass.drift.adjustment=1, min.mass=3000, peak.extraction=1, merge.copies=7, shiftPar=0.0004) stopifnot( dim(Data$X)==c(25,60) ) strsplit(Data$mzXML$parentFile, '\n') # show mzXML$parentFile record strsplit(Data$mzXML$dataProcessing, '\n') # show mzXML$dataProcessing record