A function to Group Amplification Curves According to their Shape

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.

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.

See also

metric.hausdorff, cutree, qPCR2fdata, hclust, cor

Examples

# Classify amplification curve data by Hausdorff distance
if (FALSE) {
library(qpcR)
tReem(testdat[, 1:5])
}