High-resolution Twin-Ion Metabolic Extraction
Python
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hitime
visualise
CHANGES.txt
LICENSE.txt
MANIFEST.in
NOTES.txt
README.md
setup.py

README.md

1. Introduction

HiTIME website

2. License

HiTIME is open source software, released under the 3-clause BSD license.

3. Usage

usage: hitime [-h] [--format FORMAT] [--intensityRatio R] [--rtWidth W]
              [--rtSigma RTSIGMA] [--ppm P] [--mzWidth F] [--mzSigma MZSIGMA]
              [--logFile FILENAME] [--mzDelta D] [--removeLow REMOVELOW]
              [--outDir DIRECTORY] [--noScore] [--minSample MINSAMPLE]
              inputFile outputFile

Filter mass spec data for isotope doublets.

positional arguments:
  inputFile             mass spec input data file
  outputFile            file name to save text data to

optional arguments:
  -h, --help            show this help message and exit
  --format FORMAT       file format used for input mass spec data, options
                        are: mzml; mzdata
  --intensityRatio R    ratio of intensities for a doublet (isotope
                        amount/parent amount)
  --rtWidth W           Retention Time full width at half maximum in number of
                        scans
  --rtSigma RTSIGMA     Boundary for retention time width in standard
                        deviations
  --ppm P               m/z tolerance in parts per million
  --mzWidth F           m/z full width at half maximum in parts per million
  --mzSigma MZSIGMA     Boundary for mz window in standard deviations
  --logFile FILENAME    log progress in FILENAME
  --mzDelta D           m/z difference for doublets
  --removeLow REMOVELOW
                        Remove intensity values below the given signal level
  --outDir DIRECTORY    save output in DIRECTORY, if it does not exist it will
                        be created
  --noScore             process without scoring. Use for data exploration
  --minSample MINSAMPLE
                        minimum number of data points required in each sample
                        region