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simple utility for parsing and working with NMR peak tables, including ROC analysis

Project description

nmrtoolbox

Introduction

This is a simple utility that provides modules for working with NMRPipe peak tables and performing a receiver operator characteristic (ROC) analysis to quantify the quality of the "recovered" peaks relative to a control set of "injected" peaks. The modules in this package are as follows:

  • nmrtoolbox.peak: classes for reading in peak tables (currently supports both synthetically generated and recovered peak tables from NMRPipe)
  • nmrtoolbox.roc: perform receiver operator characteristic (ROC) analysis of a recovered peak table relative to an injected peak table
  • nmrtoolbox.mask: define regions of a spectrum that contain signal or are empty
  • nmrtoolbox.util: various supporting utilities used by other modules

Applications

Example #1 - Formal Workflow

The tools in this package are utilized by the NUScon software package. You can access NUScon on the NMRbox platform (free for academic, government, and non-profit users). Running nuscon -h will provide instructions on how to run the NUScon evaluation workflow, which directly utilizes the tools presented here in the nmrtoolbox package.

Example #2 - Kick the Tires

from nmrtoolbox.roc import roc

# perform ROC analysis and specify filtering criteria for 
# cluster_type and chi2prob
my_roc = roc(
    recovered_table=<file-recovered.tab>,
    injected_table=<file-injected.tab>,
    cluster_type=1,
    chi2prob=.75,
)

# show and plot results
my_roc.print_stats()
my_roc.plot_roc()
my_roc.plot_peaks()
my_roc.plot_outliers()

The roc function supports the following filter criteria:

  • number
  • height
  • abs_height
  • roi_list
  • index
  • cluster_type
  • mask_file
  • chi2prob

Note: Filtering by mask requires the external use of NMRPipe to generate a mask file indicating where the spectrum is empty. This binary data is converted by Connjur Spectrum Translator into a "tabular" format file (i.e. plain text) which is then read in by nmrtoolbox.mask.

Changelog

v8

  • change to MIT license
  • box_radius for mask filtering is multidimensional
  • improved input options for setting carrier frequency
  • axis labels used to verify compatibility of Peak and Mask objects

v7

  • addition of roc module
  • addition of mask module

v6

  • rename package as nmrtoolbox
  • use subclasses to handle NMRPipe peak tables coming from genSimTab or from the peak picker

v5

  • new Axis class for containing metadata from peak table header

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