encu: A function to calculate numerous features from amplification...

In PCRuniversum/PCRedux: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit

A function to calculate numerous features from amplification curve data from a quantitative PCR experiment.

Description

encu (ENcode CUrves) is a function to calculate numerous features of a large amplification curve data set. The pcrfit_single is performing the analysis for a single process.

Usage

encu(data, detection_chemistry = NA, device = NA)

Arguments

data	is the data set containing the cycles and fluorescence amplitudes.
detection_chemistry	contains additional meta information about the detection chemistry (e.g., probes, intercalating dye) that was used.
device	contains additional meta information about the qPCR system that was used.

Value

gives a data.frame vector (S3 class, type of list) as output for features

The output of the encu function is identical to the pcrfit_single function.

Author(s)

Stefan Roediger, Michal Burdukiewcz

Examples

# Calculate curve features of an amplification curve data. Note that not all
# available CPU cores are used. If need set "all" to use all available cores.
# In this example the testdat data set from the qpcR package is used.
# The samples F1.1 and F1.2 are positive amplification curves. The samples
# F1.3 and F1.4 are negative.

library(qpcR)
res_encu <- encu(testdat[, 1:3])
res_encu

PCRuniversum/PCRedux documentation built on July 30, 2024, 8 p.m.