generateDesign: Generate design of microtiter plate-based synergy screening...

In ybukhman/SynergyScreen: Analyze and simulate synergy screen data

Description

Design specifies compound treatments, untreated controls and blanks that go in each well of a set of microtiter plates.

Usage

generateDesign(object, ...)

## S4 method for signature 'DREList'
generateDesign(object, dre.orientation, control.orientation,
  use.edge, digits = 3)

## S4 method for signature 'SynergyScreen'
generateDesign(object, type = "5 doses exp",
  dre.orientation = NULL, control.orientation = NULL,
  dose.series.type = NULL, use.edge = NULL, singles = T, pairs = T,
  digits = 3)

Arguments

object	an object of supported type, e.g. DREList or SynergyScreen
...	method-specific arguments: see below
dre.orientation	character. Must be set if type="custom". Specifies if dose-response experiments are to be in rows or columns. Supported values are "rows" and "columns"
control.orientation	character. Must be set if type="custom". Specifies if untreated controls are to be in rows or columns. Supported values are "rows" and "columns"
use.edge	logical. Must be set if type="custom". Specifies if wells at the edge of the plate, e.g. rows "A" and "H" and columns "1" and "12", are to be used for dose series and untreated controls or left blank.
digits	number of decimal places in dose values
type	design type. Supported types include "5 doses exp", "8 doses linear", "12 doses exp", and "custom". See Details.
dose.series.type	character type of dose series. Must be set if type="custom". Supported values are "linear" and "exp".
singles	logical: if singles = T, include dose-response experiments for individual compounds (SynergyScreen method)
pairs	logical: if pairs = T, include dose-response experiments for compound pairs (SynergyScreen method)

Details

Screen design is represented as a data frame. A SynergyScreen object has slots

Value

SynergyScreen method

returns a SynergyScreen object with populated @design, @dre_list and, if pairs=T, @synergy_experiment_list slots

DREList method

returns a data frame that represents experimental design

Methods (by class)

• DREList: Generate design from a DREList object

  Taking a DREList object as input, generate a microtiter plate design showing what to put in each well.

• SynergyScreen: Taking a SynergyScreen object as input, generate a microtiter plate design showing what to put in each well.

  This method also sets up dose-response experiment objects in object@dre_list and synergy experiment objects in object@synergy_experiment_list

See Also

SynergyScreen, DREList, DRE, SynergyExperimentList, SynergyExperiment

ybukhman/SynergyScreen documentation built on May 4, 2019, 2:31 p.m.