Maintained by ppernot
pretreatFTICR.R
scriptRaw FT-ICR DMS files are very large and are painful to analyse directly. Two reduction methods can be used and combined:
filtering the data to match as well as possible a predefined regular grid
keeping only the data that match a list of targets
Combining both methods might enable to reduce the MS size by nearly 90%, in the usual applications.
The script is controlled by the following parameters:
#====================================================
# User configuration params =========================
#====================================================
## Data and results directories
origMsDir = 'Test_FTICR_2/FTICR'
compMsDir = 'Test_FTICR_2/FTICR_compressed'
ms_type = 'fticr'
## Compress mode
compMode = c('grid','targets','grid+targets')[3]
## Grid specifications
mzMin = 70
mzMax = 250
dmz = 0.001
## Targets specifications
tgTable = 'Test_FTICR_2/targets_list.csv'
dmzTarget = 0.5 # Delta m/z to keep around target
## Short run to check ?
test = FALSE
where
origMsDir
: (string) is the path to a directory containing the
files to treat (all files within the directory will be treated).
compMsDir
: (string) is the path to a directory where the
compressed files will be stored.
ms_type
: (string) is the type of MS to treat. Only fticr
at the
moment.
compMode
: (string) compression modality, which can be grid
,
targets
or their combination grid+targets
.
mzMin
, mzMax
and dmz
: (numbers) define the regular grid used
for grid selection.
tgTable
: (string) is the path to the targets file used for targets
selection.
dmzTarget
: (number) is the half-width of the m/z interval to keep
around a target. The interval is centered on ms_ref
vales in
tgTable
. The width should be large enough to not miss the peaks,
but small enough for efficient compression…
test
: (logical) test run only, to check if data are OK.
Note: it is best to store the spectra as compressed .gz files. The disp space is well reduced and all scripts can handle them transparently.