adpsType: adpsType R6 class.

In kablag/RDML: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

adpsType R6 class.

Description

adpsType R6 class.

adpsType R6 class.

Format

An R6Class generator object.

Details

Contains matrix of amplification data. Must have three columns:

cyc

PCR cycle at which data point was collected (every cycle must have unique number).

tmp

temperature in degrees Celsius at the time of measurement (optional).

fluor

raw fluorescence intensity measured.

Inherits: rdmlBaseType.

Initialization

adpsType$new(fpoints)

Fields

fpoints

assertMatrix. Matrix with amplification data points.

Super class

RDML::rdmlBaseType -> adpsType

Methods

Public methods

• adpsType$new()

• adpsType$.asXMLnodes()

• adpsType$clone()

Inherited methods

• RDML::rdmlBaseType$copy()

• RDML::rdmlBaseType$print()

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Method new()

Usage

adpsType$new(fpoints)

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Method .asXMLnodes()

Usage

adpsType$.asXMLnodes(node.name)

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Method clone()

The objects of this class are cloneable with this method.

Usage

adpsType$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

#cycles
cyc <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40)
#fluorescence
fluo <- c(2.0172, 2.0131, 2.0035, 2, 2.0024, 2.0056, 2.0105, 2.0179,
2.0272, 2.0488, 2.0922, 2.1925, 2.3937, 2.7499, 3.3072, 4.0966,
5.0637, 6.0621, 7.0239, 7.8457, 8.5449, 9.1282, 9.6022, 9.9995,
10.2657, 10.4989, 10.6813, 10.8209, 10.9158, 10.9668, 11.0053,
11.0318, 11.0446, 11.044, 11.0052, 10.9671, 10.9365, 10.9199,
10.897, 10.8316)
#temperature
temp <- c(55, 55, 55, 55, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55,
55, 55, 55, 55, 55, 55, 55, 55, 56, 55, 55, 55, 55, 55, 55, 55,
55, 55, 55, 55, 55, 55, 55, 55, 55)

#combine all variables into a proper object
data <- data.frame(cyc = cyc, tmp = temp, fluor = fluo)

#create adps object
adpsType$new(data)

#create adps object without temperature data
adpsType$new(data[, -2])

kablag/RDML documentation built on Oct. 20, 2022, 5:47 a.m.