clusterAverages: calculates cluster averages
In raim/segmenTools: Tools for Functional Genome Exploration

clusterAverages

R Documentation

calculates cluster averages

calculates average values and distributions for each cluster and time point of a time series

clusterAverages(ts, cls, cls.srt, avg = "median", q = 0.9, rm.inf = TRUE)

`ts`	a matrix of time series, with time points in columns
`cls`	a clustering of the time series, `length(cls)` must equal `nrow(cls)`
`cls.srt`	optional sorting of the clusters
`avg`	a function (or the name of a function as a string) for calculating an ‘average’ value for each cluster; default is the `median` ## @param dev a function for calculating deviation from the the average, ## default is the standard deviation (‘sd’)
`q`	either numeric (0.5-1, or 0), or a string. If numeric it indicates the fraction of data shown as transparent ranges, e.g. `q=0.9` indicates that 90 ranges, i.e. the 5 borders, and for q=0.5 the ranges correspond to the box limits in a boxplot. If q is a string it must be a function name for calculating variance (eg. "sd", "var"), which will be added and subtracted from the average (argument `avg`) for high and low data cut-offs.
`rm.inf`	remove infinite values (e.g. from log transformations)