make_si {recountmethylation} | R Documentation

## make_si

### Description

Make search index from table of hashed features. Additional details about the hnswlib search index parameters (e..g 'space_val', 'efc_val', 'm_val', and 'ef_val') can be found in the Python package docstrings and ReadMe.

### Usage

    make_si(
      fh_csv_fpath,
      si_fname = "new_search_index.pickle",
      si_dict_fname = "new_index_dict.pickle",
      threads = 4,
      space_val = "l2",
      efc_val = 2000,
      m_val = 1000,
      ef_val = 2000
    )

### Arguments

`fh_csv_fpath` | Name/path of csv (e.g. a table of hashed features) containing data for the index (required, string, "bvaltest.csv", where rows = samples, cols = features).
`si_fname` | Name of new search index file to save (required, string, "new_search_index.pickle")
`si_dict_fname` | Name of new index dictionary, with string labels, to save (required, string, "new_index_dict.pickle").
`threads` | Number of threads for processing new index (required, int, 4).
`space_val` | Space value for new search index (required, valid string, l2').
`efc_val` | EFC value for the index (required, int, 2000).
`m_val` | M value for the index (required, int, 1000).
`ef_val` | EF value for the index (required, int, 2000).

### Value

Boolean, TRUE if new search index and dictionary created, FALSE if creating the new search index and dictionary files failed, otherwise NULL.

### Examples

    # fh_csv_fpath <- system.file("extdata", "fhtest",
    # package = "recountmethylation")
    # fh_csv_fpath <- file.path(fh_csv_fpath, "bval_fn.csv")
    # make_si(fh_csv_fpath)

[Package recountmethylation version 1.4.5 Index]