__ __ _ _ _ _ _ _____ _
| \/ | | | | | | (_) | / ____| |
| \ / | ___| |_ __ _| |__ ___ | |_| |_ ___ ___ | | | | ___ __ _ _ __ ___ _ __
| |\/| |/ _ \ __/ _` | '_ \ / _ \| | | __/ _ \/ __| | | | |/ _ \/ _` | '_ \ / _ \ '__|
| | | | __/ || (_| | |_) | (_) | | | || __/\__ \ | |____| | __/ (_| | | | | __/ |
|_| |_|\___|\__\__,_|_.__/ \___/|_|_|\__\___||___/ \_____|_|\___|\__,_|_| |_|\___|_|
Metabolites Cleaner is a tool to tidy up compounds list to simplify further metabolomics analysis
Removes Targert
and Orthogonal
as well as removes metabolites found in the folder Rejected
from the NIST.txt file. Provides detailed info of the processing done.
Reject unwanted metabolites from the Excel workbook. Creates a worksheet with rejected metabolites.
Cleans metabolite names in the excel table.
- Compatible with Windows command prompt. Just double click
Metabolites Cleaner.bat
to run. - It automatically checks if R is installed and finds correct path to it. If not R found then it downloads and installs one.
Note! By default it requires installed R in C'\Program Files\R...
directory.
- It automatically downloads and installs all required R packages.
- Select an option to run
Note! Make sure Metabolites Cleaner folder and working folder with input files are in folders named with no special characters and spaces. Avoid use spaces. Use _
(underline) instead.
- Navigate to the png files repository of the metabolites peaks.
- Create
Rejected
folder in the root of the png files repository. - All png files you want to discard move to
Rejected
folder. - Select
RDA_Target_NIST.txt
file. - By default it removes
Targert
,Orthogonal
and entries found inRejected
folder. Modifyconfig.yml
. To activate function set 1 to a property, to deactivate set 0.
remove_Target: 1
remove_Orthogonal: 1
remove_Recursion: 0
remove_rejceted: 1
- Creates
RDA_Target_NIST_CLEAN.txt
file in the root folder. - Removes selected entry types.
- Finds matches of the png names in the
Rejected
folder in the NIST file and removes such entries. - Finds exceptions and ignores errors so it will ends properly.
- Provides detailed info about the processions was done.
- Navigate to the png files repository of the metabolites peaks.
- Create
Rejected
folder (if such does not exist) in the root folder. - All png files you want ot discard move to
Rejected
folder. - Select excel file.
Excel Cleaner
by default uses worksheetIntegrated Unimodal 1
. You can modify it inconfig.yml
file following variable:
xlsx_sheet: Integrated Unimodal 1
- In
config.yml
select search algorithm to use, where search by index set 0, search by name set 1:
search_algorithm: 1
- Select input file with pop up window.
Metabolites Cleaner
createsRDA_Target_Data_Model_CLEAN.xlsx
file that is a duplicate fileRDA_Target_Data_Model.xlsx
.- In the
RDA_Target_Data_Model_CLEAN.xlsx
worksheetIntegrated Unimodal 1
moves all columns of metabolites that found inRejected
folder toRejected
worksheet. - Duplicates worksheet clean
Integrated Unimodal 1
and names itCLEAN NAMES
. - Worksheet
CLEAN NAMES
cleans all head names of columns with metabolites.
- Select excel file to fix component names.
- Done.
By default it uses worksheet
Integrated Unimodal 1
. You can modify it inconfig.yml
file following variable:
xlsx_sheet: Integrated Unimodal 1
- Removes index if such exists:
S227_GLUCOSE_6_PHOSPHATE_MEOX_6TMS_minor___2
->_GLUCOSE_6_PHOSPHATE_MEOX_6TMS_minor___2
. - Removes
nTMS
, wheren
isn
character and digit and characters followed afternTMS
:_GLUCOSE_6_PHOSPHATE_MEOX_6TMS_minor___2
->_GLUCOSE_6_PHOSPHATE_MEOX_
. - Removes
MEOX
and characters followed afterMEOX
:_GLUCOSE_6_PHOSPHATE_MEOX_
->_GLUCOSE_6_PHOSPHATE_
. - Removes unwanted characters such as spaces and underlines:
_GLUCOSE_6_PHOSPHATE_
->GLUCOSE 6 PHOSPHATE
. - Replaces uppercase to lowercase:
GLUCOSE 6 PHOSPHATE
->Glucose 6 phosphate
.
Metabolites Cleaner tool requires listed below open source CRAN packages:
dplyr
readxl
yaml
rio
openxlsx
progress
R.utils
stringdist
yaml
stringr
Note! Run \res\OS_environment.bat
to switch OS_environment
key to run Metabolites Cleaner in Windows terminal.