sfp: sfp

In BenjaminChittick/Plate-Based-Diversity:

Description

Converts ECFP hash codes into a sparse matrix by arbitrarily assigning them as indices.

Usage

sfp(data, cpd.identifier)

Arguments

data	data.table containing compound identifier and fingerprint hash
cpd.identifier	character string identifying compounds: Broad ID, InChIKey, etc...

Examples

hashes <- round(rnorm(120, 100000000, 1000), 1)
compounds <- data.table('ECFP_4[1]' = sample(hashes, 100, replace=TRUE),
                        'ECFP_4[2]' = sample(hashes, 100, replace=TRUE),
                        'ECFP_4[3]' = sample(hashes, 100, replace=TRUE),
                        'ECFP_4[4]' = sample(hashes, 100, replace=TRUE),
                        'ECFP_4[5]' = sample(hashes, 100, replace=TRUE))
compounds$InChIKey <- sapply(1:dim(compounds)[1], function(x)
                             paste(sample(LETTERS, 10, replace=TRUE), collapse=''))
sparseFP <- sfp(compounds, cpd.identifier='InChIKey')
sparseFP[1:10, 1:15]

BenjaminChittick/Plate-Based-Diversity documentation built on May 5, 2019, 2:41 p.m.