R/combineTrackll.R

In sheng-liu/sojourner: Statistical analysis of single molecule trajectories

#### combineTrackll.R Wu Lab, Johns Hopkins University Author: Xiaona Tang
#### Date: Sep 20, 2017

## combineTrackll-methods
##' @name combineTrackll
##' @aliases combineTrackll
##' @title combineTrackll
##' @rdname combineTrackll-methods
##' @docType methods
##' @description Combine multiple tracklls into one trackll.
##'
##' @usage
##'
##' combineTrackll(trackll,name='combined trackll',merged=TRUE)
##'
##' @param trackll The tracklls to be combined together.
##' @param name a character string given to set the 'names' attribute
##' for the combined trackll
##' @param merged An Logical indicate if the tracklls to combine are 
##' merged or not.
##' @return
##' \itemize{
##' \item{trackll:} combined trackll.
##' }
##' @details Combine multiple track lists (tracklls) from multiple folders
##' into one trackll, i.e. combining track infomation from files in multiple 
##' folders (replicates) together as if they are in one folder. The tracklls
##' can be either merged or un-merged.
##' 
##' The name argument sets the 'names' attribute for the combined trackll, 
##' which will be used in the same way as the folder names for the original
##' tracklls, e.g., displayed as legend when plotting Dcoef or MSD for 
##' the combined trackll. 
##'
##'
##' @examples
##'
##' # Generate trackll, and process, 
##' # e.g. mask region of interest, merge tracks from multiple files.
##' folder1=system.file('extdata','HSF',package='sojourner')
##' trackll1=createTrackll(folder1,input=3, cores = 2)
##' trackll1=maskTracks(folder1,trackll1)
##' trackll1=mergeTracks(folder1,trackll1)
##' 
##' folder2=system.file('extdata','HSF_2',package='sojourner')
##' trackll2=createTrackll(folder2,input=2, cores = 2)
##' trackll2=maskTracks(folder2,trackll2)
##' trackll2=mergeTracks(folder2,trackll2)
##'
##' # Combine the tracklls together, input trackll names when prompted,
##' trackll=combineTrackll(trackll=c(trackll1,trackll2),merged=TRUE)

##' @export combineTrackll
############################################################################## 


combineTrackll <- function(trackll, name = "combined trackll", merged = TRUE) {
    totalTracklls <- as.numeric(length(trackll))
    temp <- c()
    if (merged == TRUE) {
        for (i in seq_len(totalTracklls)) {
            temp <- append(temp, trackll[i][[1]])
        }
        temp <- list(temp)
        names(temp) <- name
    } else if (merged == FALSE) {
        for (i in seq_len(totalTracklls)) {
            temp <- append(temp, trackll[i])
        }
    } else {
        cat("Wrong input. Start again.\n")
        stop()
    }
    return(temp)
    
}