parseTraj: Reads in files containing trajectory data

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

View source: R/helpers.R

Description

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

Usage

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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

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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

Example output

Loading required package: ggplot2
Loading required package: changepoint
Loading required package: zoo

Attaching package:zooThe following objects are masked frompackage:base:

    as.Date, as.Date.numeric

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.
Loading required package: wavethresh
Loading required package: MASS
WaveThresh: R wavelet software, release 4.6.8, installed

Copyright Guy Nason and others 1993-2016

Note: nlevels has been renamed to nlevelsWT

Loading required package: tseries
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
Loading required package: pvclust
Loading required package: fBasics
Loading required package: timeDate
Loading required package: timeSeries

Attaching package:timeSeriesThe following object is masked frompackage:zoo:

    time<-

Loading required package: grid
Loading required package: reshape
Loading required package: scales
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

deltaGseg documentation built on Nov. 8, 2020, 8:06 p.m.