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

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

Description

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

Usage

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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)

See Also

SynergyScreen, DREList, DRE, SynergyExperimentList, SynergyExperiment


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