gen_annotation: Compute the annotation of the progrex index

In CampaR1: Trajectory Analysis

Description

gen_annotation is able to annotate the progrex index using the mean first passage time between groups of snapshots on the progrex index. This function will produce a file (e.g. "REPIX_000000000001.dat") that contains all the information about progress index and annotations and it can be used to plot the sapphire plot using sapphire_plot.

Usage

gen_annotation(ret_data, local_cut_width = NULL, snap_start = NULL)

Arguments

ret_data	This input must be the output from the function gen_progindex.
local_cut_width	This variable defines the width for a 3 groups annotation of the progrex index.
snap_start	Starting snapshot. It must be the same as in gen_progindex. Best to leave not assigned.

Details

For details, please refer to the main documentation of the original campari software http://campari.sourceforge.net/documentation.html.

See Also

gen_progindex, sapphire_plot.

Examples

adjl <- mst_from_trj(trj = matrix(rnorm(1000), nrow = 100, ncol = 10))
adjl2 <- contract_mst(adjl = adjl)
ret<-gen_progindex(adjl = adjl2)
gen_annotation(ret_data = ret, local_cut_width = 10)

CampaR1 documentation built on May 30, 2017, 2:51 a.m.