R/xcms_df.R

In tkimhofer/msbrowser: Viz tool for xcms peak picking parameter optimisation

# Read-in LC-MS file (xcms) and extract raw scan data and create dataframe
# param raw_xcms xcms data object
# return data frame mz, Int, scan, scantime
#' @importFrom xcms xcmsRaw

xcms_df <- function(raw_xcms) {
    message("extract xcms raw data")
    df_xcms <- data.frame(mz = raw_xcms@env$mz, Int = raw_xcms@env$intensity)
    ndp <- length(raw_xcms@env$mz)
    idx.trans <- which(raw_xcms@env$mz[-1] < raw_xcms@env$mz[-ndp])  # every new scan starts with low mz
    idx.scans <- cbind(c(0, idx.trans) + 1, c(idx.trans, ndp))  # create df of indices (one scan per row)
    df_xcms$scan <- unlist(lapply(seq_len(nrow(idx.scans)), function(i) {
        rep(i, diff(idx.scans[i, ]) + 1)
    }))
    df_xcms$scantime <- raw_xcms@scantime[df_xcms$scan]  # add scantime (s)
    return(df_xcms)
}