parseTraj {deltaGseg}R Documentation

Reads in files containing trajectory data

Description

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

Usage

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

Arguments

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.

Details

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.

Value

A 'Trajectories' object.

Author(s)

Diana H.P. Low, Efthimios Motakis

References

None.

See Also

Trajectories-class

Examples

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

[Package deltaGseg version 1.26.0 Index]