fp.read, fp.read.to.matrix {fingerprint}R Documentation

Functions to read fingerprints from files

Description

fp.read reads in a set of fingerprints from a file. Fingerprint output from the CDK, MOE and BCI can be handled.

Each fingerprint is represented as an integer vector whose elements indicate which positions of the bit string are set to 1. Since the fingerprint is simply a numeric() most functions will require the length of the actual bit string to be passed in. fp.read returns a list structure, each element being a fingerprint vector.

fp.read.to.matrix is a utility function that reads the fingerprints directly to matrix form (columns are the bit positions and the rows are the objects whose fingerprints have been evaluated)

Usage

fp.read(f='fingerprint.txt', lf=cdk.lf, header=FALSE)
fp.read.to.matrix(f='fingerprint.txt', size=1024, lf=cdk.lf, header=FALSE)

Arguments

f File containing the fingperprints
size The length of the fingerprints being considered
lf A line reading function that parses a single line from a fingerprint file. Currently, two such functions are provided that parse the fingerprints from the output of the CDK and MOE respectively. See cdk.lf and moe.lf
header Indicates whether the first line of the fingerprint file is a header line

Value

A list or matrix of fingerprint vectors

Author(s)

Rajarshi Guha rguha@indiana.edu

See Also

cdk.lf, moe.lf, bci.lf


[Package fingerprint version 1.6 Index]