R/clampfit.R

In scbursts: Single Channel Bursts Analysis

#' Read a .xlsx file output from clampfit
#' 
#' Read a .xlsx file output from clampfit. Result is a list of "segments", which is a dataframe extra data. See "segment" for more details. Converts millisecond dwells to seconds.
#'
#' @param filename Filename to read from
#' @param separating_factor In lieu of a known time between segments, seperate with a multple of the longest dwell.
#' @param header Does the file include a header?
#' @return A list of bursts (possibly a singleton)
#' @examples
#' 
#' infile <- system.file("extdata", "example1_clampfit.xlsx", package = "scbursts")
#' dwells <- clampfit.read(infile)
#' head(dwells)
#' 
#' @export
#' @importFrom readxl read_excel 
#' @importFrom tibble as_tibble
clampfit.read <- function(filename, separating_factor=1000, header=FALSE) {

    i_read           <- read_excel(filename,sheet=1,col_names=header) #read in the .xlsx file
    names(i_read)[3] <- 'states'
    names(i_read)[9] <- 'dwells'
    dwells           <- tibble::as_tibble(i_read[9][,1])$dwells # column 9 are the dwells
    dwells           <- dwells / 1000 # milliseconds to seconds
    max_dwells       <- separating_factor
    max_dwells       <- max(max(dwells)*separating_factor, max_dwells)
    states           <- tibble::as_tibble(i_read[3][,1])$states # column 3 are the conductance levels

    ## Remove leading 0
    if (states[1] == 0) {
        warning("Removing leading 0 dwell.")
        states  <- states[2:length(states)]
        dwells  <- dwells[2:length(dwells)]
    }
    ## Remove trailing 0
    if (states[length(states)] == 0) {
        warning("Removing trailing 0 dwell.")
        states  <- states[1:length(states)-1]
        dwells  <- dwells[1:length(dwells)-1]
    }
        
    brst             <- list()
    brst[[1]]        <- segment.create(states,dwells,seg=1,start_time=0,name=util.basename(filename))
    brst             <- bursts.start_times_update(brst,gaps=rep(max_dwells,0))
    return(brst)

}