vignette/sets/chembl21/scripts/4__activity_types.R

In momeara/data_repo: Load bioinformatics datasets into a local database

# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:


# help parse chembl activities
library(plyr)
library(dplyr)

activity_unit_transforms = c(
	# SI molar units
	'fM'=1e-6, 'pM'=1e-3, 'nM'=1, 'uM'=1e3, 'mM'=1e6, 'M'=1e9,
	# SI moles per ml
	'fmol/ml'=1e-3, 'pmol/ml'=1, 'nmol/ml'=1e3, 'umol/ml'=1e9, 'mmol/ml'=1e12,
	# per mole
	'M-1'=1e-9)
activity_units <- names(activity_unit_transforms)

minus_log <- function(x) 10^(9-x)
plus_log <- function(x) 10^(9+x)
identity <- function(x) x

activity_type_transforms = c(
	# Kd
	'Kb'=identity,
	'pKb'=minus_log,
	'-Log Kb'=minus_log,
	'Log 1/Kb'=minus_log,
	'log(1/Kb)'=minus_log,
	'Log Kb'=plus_log,
	'logKb'=plus_log,

	# Kd
	'Kd'=identity,
	'pKd'=minus_log,
	'-Log Kd'=minus_log,
	'Log 1/Kd'=minus_log,
	'log(1/Kd)'=minus_log,
	'Log Kd'=plus_log,
	'logKd'=plus_log,

	'-Log KD'=minus_log,


	# Ki
	'Ki'=identity,
	'pKi'=minus_log,
	'-Log Ki'=minus_log,
	'Log 1/Ki'=minus_log,
	'log(1/Ki)'=minus_log,
	'Log Ki'=plus_log,
	'logKi'=plus_log,


	# Concentration required to elicit a 50% response in an in vitro assay
	'AC50'=identity,
	'-Log AC50'=minus_log,
	'Log 1/AC50'=minus_log,
	'log(1/AC50)'=minus_log,
	'Log AC50'=plus_log,
	'logAC50'=plus_log,

	# anesthesia dose
	'AD50'=identity,
	'-Log AD50'=minus_log,
	'Log 1/AD50'=minus_log,
	'log(1/AD50)'=minus_log,
	'Log AD50'=plus_log,
	'logAD50'=plus_log,

	 # cytotoxcity
	'CC50'=identity,
	'-Log CC50'=minus_log,
	'Log 1/CC50'=minus_log,
	'log(1/CC50)'=minus_log,
	'Log CC50'=plus_log,
	'logCC50'=plus_log,

	# effective concentration (for antagonists)
	'EC50'=identity,
	'pEC50'=minus_log,
	'-Log EC50'=minus_log,
	'Log 1/EC50'=minus_log,
	'log(1/EC50)'=minus_log,
	'Log EC50'=plus_log,
	'logEC50'=plus_log,

	'EC90'=identity,
	'pEC90'=minus_log,
	'-Log EC90'=minus_log,
	'Log 1/EC90'=minus_log,
	'log(1/EC90)'=minus_log,
	'Log EC90'=plus_log,
	'logEC90'=plus_log,

	# effective dose (for agonists)
	'ED50'=identity,
	'pED50'=minus_log,
	'-Log ED50'=minus_log,
	'Log 1/ED50'=minus_log,
	'log(1/ED50)'=minus_log,
	'Log ED50'=plus_log,
	'logED50'=plus_log,

	# concentration for 50% of maximal inhibition of cell proliferation
	'GI50'=identity,
	'pGI50'=minus_log,
	'-Log GI50'=minus_log,
	'Log 1/GI50'=minus_log,
	'log(1/GI50)'=minus_log,
	'Log GI50'=plus_log,
	'logGI50'=plus_log,

	'IA50'=identity,
	'pIA50'=minus_log,
	'pIA50'=minus_log,
	'-Log IA50'=minus_log,
	'Log 1/IA50'=minus_log,
	'log(1/IA50)'=minus_log,
	'Log IA50'=plus_log,
	'logIA50'=plus_log,

	'IC50'=identity,
	'pIC50'=minus_log,
	'-Log IC50'=minus_log,
	'Log 1/IC50'=minus_log,
	'log(1/IC50)'=minus_log,
	'Log IC50'=plus_log,
	'logIC50'=plus_log,

	'IC60'=identity,
	'pIC60'=minus_log,
	'-Log IC60'=minus_log,
	'Log 1/IC60'=minus_log,
	'log(1/IC60)'=minus_log,
	'Log IC60'=plus_log,
	'logIC60'=plus_log,

	'IC70'=identity,
	'pIC70'=minus_log,
	'-Log IC70'=minus_log,
	'Log 1/IC70'=minus_log,
	'log(1/IC70)'=minus_log,
	'Log IC70'=plus_log,
	'logIC70'=plus_log,

	'IC80'=identity,
	'pIC80'=minus_log,
	'-Log IC80'=minus_log,
	'Log 1/IC80'=minus_log,
	'log(1/IC80)'=minus_log,
	'Log IC80'=plus_log,
	'logIC80'=plus_log,

	'IC90'=identity,
	'pIC90'=minus_log,
	'-Log IC90'=minus_log,
	'Log 1/IC90'=minus_log,
	'log(1/IC90)'=minus_log,
	'Log IC90'=plus_log,
	'logIC90'=plus_log,

	'IC95'=identity,
	'pIC95'=minus_log,
	'-Log IC95'=minus_log,
	'Log 1/IC95'=minus_log,
	'log(1/IC95)'=minus_log,
	'Log IC95'=plus_log,
	'logIC95'=plus_log,

	'IC99'=identity,
	'pIC99'=minus_log,
	'-Log IC99'=minus_log,
	'Log 1/IC99'=minus_log,
	'log(1/IC99)'=minus_log,
	'Log IC99'=plus_log,
	'logIC99'=plus_log,

	'IC100'=identity,
	'pIC100'=minus_log,
	'-Log IC100'=minus_log,
	'Log 1/IC100'=minus_log,
	'log(1/IC100)'=minus_log,
	'Log IC100'=plus_log,
	'logIC100'=plus_log,

	'ID50'=identity,
	'pID50'=minus_log,
	'-Log ID50'=minus_log,
	'Log 1/ID50'=minus_log,
	'log(1/ID50)'=minus_log,
	'Log ID50'=plus_log,
	'logID50'=plus_log,

	 # lethal dose
	'LD50'=identity,
	'-Log LD50'=minus_log,
	'Log 1/LD50'=minus_log,
	'log(1/LD50)'=minus_log,
	'Log LD50'=plus_log,
	'logLD50'=plus_log,

	# maximum inhibitory concentration
	'MIC'=identity,
	'MIC50'=identity,
	'MIC90'=identity)
activity_types <- names(activity_type_transforms)


# there is probably a better way....
normalize_activity_value <- function(type, unit, value){
	llply(1:length(type), function(i){
		tryCatch({
			activity_type_transforms[[type[[i]] ]](value[[i]] ) *
			activity_unit_transforms[[unit[[i]] ]]
		}, error= function(e){
			print(paste0("error on row ", i, "\n", e))
			stop()
		})
	}) %>% unlist
}