PCRedux (version 1.1-2)

tReem: 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

See Also

metric.hausdorff, cutree, qPCR2fdata, hclust, cor

Examples

# NOT RUN {
# Classify amplification curve data by Hausdorff distance
# }
# NOT RUN {
library(qpcR)
tReem(testdat[, 1:5])
# }