get_fingerprint_mask: Calculate mask to exclude molecular fingerpints given a set...

In bachi55/rcdkTools: rcdkTools

Description

Given a binary fingerprint matrix a mask is calculated to exclude fingerprints:

• with the same value across the dataset

• with low variance, e.g. fp_i = 1 in 90% of the data

• which are redunant, e.g. fp_i = 1 <=> fp_j = 1

where fp_i is the i'th fingerprint definition.

Usage

get_fingerprint_mask(fps, remove_single_value = TRUE,
  remove_redundant = TRUE, remove_low_variance = TRUE,
  low_variance_tshd = 0.9)

Arguments

fps	binary matrix, shape (n_samples x n_fingerprints), e.g. the output of fingerprints_to_matrix.
remove_single_value	binary, exclude fps with always the same value
remove_redundant	binary, exclude redundant fps
remove_low_variance	binary, exlcude fps with low variance
low_variance_tshd	scalar, threshold for low variance (default = 0.9, i.e. fps where >=90% of the examples have the same value are removed)

Value

binary vector (1 x n_fingerpints):

• TRUE: keep fingerprint

• FALSE: exclude fingerprint

bachi55/rcdkTools documentation built on Nov. 3, 2019, 2:06 p.m.