tReem: A function to Group Amplification Curves According to their...

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

A function to Group Amplification Curves According to their Shape

Description

tReem is a function to group amplification curves from a quantitative PCR experiment according to their shape. Either the Pearson correlation coefficient or the Hausdorff distance is used as measure. In most cases the grouping based on the Pearson correlation coefficient is sufficient. The grouping based on the Hausdorff distance can be very slow for large data sets.

Usage

tReem(data, cor = TRUE, k = 2)

Arguments

data	is the cycle dependent fluorescence amplitude (y-axis).
cor	is a logical parameter. If set true, the Pearson correlation is used as distance measure. If set FALSE the Hausdorff distance will be used.
k	an integer scalar or vector with the desired number of groups.

Value

gives a data.frame (S3 class, type of list) as output for the manual analyzed data

Author(s)

Stefan Roediger, Andrej-Nikolai Spiess

See Also

metric.hausdorff, cutree, qPCR2fdata, hclust, cor

Examples

# Classify amplification curve data by Hausdorff distance

library(qpcR)
tReem(testdat[, 1:5])

PCRedux documentation built on May 11, 2022, 5:18 p.m.