methylcheck.combine_mds

methylcheck.combine_mds(*args, **kwargs)

To combine (or segment) datasets for multidimensional scaling analysis

Use this function on multiple dataframes to combine datasets, or to visualize parts of the same dataset in separate colors. It is a wrapper of methylcheck.beta_mds_plot() and applies multidimensional scaling to cluster similar samples based on patterns in probe values, as well as identify possible outlier samples (and exclude them).

• combine datasets,
• run MDS,
• see how each dataset (or subset) overlaps with the others on a plot,
• exclude outlier samples based on a composite cutoff box (the average bounds of the component data sets)
• calculate the percent of data excluded from the group

• *args:

  • pass in any number of pandas dataframes, and it will combine them into one mds plot.
  • alternatively, you may pass in a list of filepaths as strings, and it will attempt to load these files as pickles.

  but they must be pickles of pandas dataframes containing beta values or m-values

• silent: (default False)

  (automated processing mode) if True, suppresses most information and avoids prompting user for anything. silent mode processes data but doesn’t show the plot.

• save: (default False)

  if True, saves the plot png to disk.

• verbose: (default False)

  if True, prints extra debug information to screen or logger.

• filter_stdev:

  how broadly should you retain samples? units are standard deviations, defaults to 1.5 STDEV. if you increase this number, fewer outlier samples will be removed.

• returns a dataframe of transformed samples