parseTraj: Reads in files containing trajectory data
In deltaGseg: deltaGseg

Description Usage Arguments Details Value Author(s) References See Also Examples

Reads in files with 2-column, space-separated numerical values containing 1:time points, 2:trajectory(free binding energies).

1	parseTraj(path = getwd(), files = NULL,fromfile=TRUE)

`path`	Directory containing trajectory files.
`files`	Character vector of filenames to read. If not provided, will read all files in given directory and treat them as a set. Can also be used to read in variables if given as list.
`fromfile`	Logical. If set to FALSE, the files parameter will be used to read in variables.

This is an initialization function for the deltaGseg package. It reads the trajectory files (input) and reports the a short description of the file, the Augmented Dickey-Fuller test p-values for each trajectory in the set and the data plot. The input files should be in tab delimited form with 2 columns: the first column contains the time points 1, 2, ..., T and the second the free binding energies at each time point.

A 'Trajectories' object.

Diana H.P. Low, Efthimios Motakis

None.

Trajectories-class

traj1<-parseTraj(path=system.file("extdata",package="deltaGseg"),files=c("D_GBTOT1","D_GBTOT2","D_GBTOT3"))
traj1  #prints summary of traj1 object

# using parseTraj for existing variables ##
subtraj<-getTraj(traj1)[[1]] #extracts first trajectory in the above series
traj2<-parseTraj(files=list(subtraj),fromfile=FALSE)
traj2

Loading required package: ggplot2
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Successfully loaded changepoint package version 2.2.2
 NOTE: Predefined penalty values changed in version 2.2.  Previous penalty values with a postfix 1 i.e. SIC1 are now without i.e. SIC and previous penalties without a postfix i.e. SIC are now with a postfix 0 i.e. SIC0. See NEWS and help files for further details.
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WaveThresh: R wavelet software, release 4.6.8, installed

Copyright Guy Nason and others 1993-2016

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Loading required package: grid
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class: Trajectories
	Source: /usr/lib/R/site-library/deltaGseg/extdata/
	Names: D_GBTOT1 D_GBTOT2 D_GBTOT3
	Trajectories: 3
	Points per trajectory: 5000 5000 5000 
	adf p-values: 0.01 0.01 0.07872805

Available slots: path filenames trajlist avd
class: Trajectories
	Source: /work/tmp/
	Names: 1
	Trajectories: 1
	Points per trajectory: 5000 
	adf p-values: 0.01

Available slots: path filenames trajlist avd