findSynergies: Find pairs of compounds that show synergy or antagonism
In ybukhman/SynergyScreen: Analyze and simulate synergy screen data

Description Usage Arguments Details Value Methods (by class) See Also Examples

Find pairs of compounds that show synergy or antagonism

findSynergies(object, ...)

## S4 method for signature 'SynergyScreen'
findSynergies(object, statistic, threshold, direction,
  model = NULL)

`object`	object of class SynergyScreen
`...`	method-specific arguments: see below
`statistic`	type of statistic to use to find synergistic or antagonistic compound pairs. Can be "min", "max", "mean" or "median".
`threshold`	threshold value that needs to be surpassed by the statistic
`direction`	can be "higher" or "lower". See Details.
`model`	character. Only consider results from the specified model. If NULL, consider all models.

This function filters the output of synergy_data(object) to report only compounds that are synergistic or antagonistic. This is done by computing a statistic of the set of interaction index values for each pair of compounds and comparing it to the threshold.

Example 1. To find pairs of compounds that show consistent synergy for all analyzed effect sizes, one may use statistic = "max", threshold = 0.7 and direction = "lower". This will select pairs of compounds whose interaction index does not exceed 0.7.

Example 2. To find pairs of compounds that show strong synergy that may or may not be consistent for all effect sizes, one may use statistic = "min", threshold = 0.3 and direction = "lower". This will select pairs of compounds whose interaction index is below 0.3 for at least one effect size.

object of type SynergyData

SynergyScreen: Find pairs of compounds that show synergy or antagonism

SynergyScreen, synergy_data

data(sim15_screen3)

#  Find strong synergies
findSynergies(sim15_screen3, statistic="max", threshold=0.5, direction="lower")

#  Find strong antagonisms
findSynergies(sim15_screen3, statistic="min", threshold=2, direction="higher")