Start introducing inv_k0

R/aaa-AllGenerics.R

@@ -242,3 +242,19 @@ setGeneric("baseline<-", function(object, value) standardGeneric("baseline<-"))
 #'
 #' @export
 setGeneric("integratePeaks", function(object, ...) standardGeneric("integratePeaks"))
+
+#' @describeIn GCIMS-generics get inverse reduced mobility
+#' @param object An object to get its inverse reduced mobility
+#' @param ... Additional arguments for downstream methods
+#' @return The object with reduced inverse mobility
+#'
+#' @export
+setGeneric("get_inv_k0", function(object, ...) standardGeneric("get_inv_k0"))
+
+#' @describeIn GCIMS-generics get retention index
+#' @param object An object to get its retention index
+#' @param ... Additional arguments for downstream methods
+#' @return The object with retention index
+#'
+#' @export
+setGeneric("get_ri", function(object, ...) standardGeneric("get_ri"))

R/aaa-class-GCIMSDataset.R

@@ -79,6 +79,10 @@ GCIMSDataset <- R6::R6Class("GCIMSDataset",
     dt_ref = NULL, # numeric or NULL
     #' @field rt_ref A numeric retention time of reference
     rt_ref = NULL, # numeric or NULL
+    #' @field inv_k0_ref A numeric inverse reduced mobility reference
+    inv_k0_ref = NULL,
+    #' @field ri_ref A numeric retention index reference
+    ri_ref = NULL,
     #' @field userData A list to store arbitrary data in the dataset
     userData = list(), # list
     # Methods:

R/aaa-class-GCIMSSample.R

@@ -14,6 +14,8 @@
 #' @slot retention_time numeric. (required)
 #' @slot data matrix A matrix with drift time in the rows and retention time
 #'  in columns. (required)
+#' @slot inverse_reduced_mobility 1/K0 (calculated from drift_time)
+#' @slot retention_index numeric. (calculated from retention_time and references)
 #' @slot gc_column character. (optional) The type of chromatographic column used
 #' @slot drift_tube_length numeric (optional) The length of the drift tube, in mm
 #' @slot drift_gas character. (optional) The drift gas used (e.g "nitrogen")
@@ -52,6 +54,8 @@ methods::setClass(
     drift_time = "numeric",
     retention_time = "numeric",
     data = "matrix", # [dt, rt]
+    inverse_reduced_mobility = "numeric",
+    retention_index = "numeric",
     gc_column = "character",
     drift_gas = "character",
     drift_tube_length = "numeric",

R/get_inv_k0-GCIMSDataset.R

@@ -0,0 +1,12 @@
+methods::setMethod(
+  "get_inv_k0",
+  "GCIMSDataset",
+  function(object){
+    delayed_op <- DelayedOperation(
+      name = "get_inverse_reduced_mobility",
+      fun = get_inv_k0
+    )
+    object$appendDelayedOp(delayed_op)
+    invisible(object)
+  }
+)

R/get_inv_k0-GCIMSSample.R

@@ -0,0 +1,25 @@
+methods::setMethod(
+  "get_inv_k0",
+  "GCIMSSample",
+  function(object)  {
+    if (is.null(object@params$`nom Drift Potential Difference`$value) |
+        is.null(object@params$`Temp 1 setpoint`$value)|
+        is.null(object@params$`Pressure Ambient`$value) |
+        length(object@drift_tube_length) == 0
+        ){
+      stop("IMS Voltage, IMS Tube length, IMS Tempreature and pressure are
+      needed to calculate the inverse reduced mobility ")
+    }
+    drift_time <- object@drift_time / 1000 # in ms to s
+    Voltage_ims <- object@params$`nom Drift Potential Difference`$value # in V
+    tube_length_cm <- object@drift_tube_length / 10 # in mm to cm
+    ims_temp_k <- object@params$`Temp 1 setpoint`$value + 273.15 # in °C
+    pressure_ims <- mean(as.numeric(strsplit(
+      object@params$`Pressure Ambient`$value, " ")[[1]]), na.rm = TRUE) #in Pa
+    K0 <- (0.0027315 * (tube_length_cm ^ 2) * pressure_ims) /
+          (Voltage_ims* drift_time * ims_temp_k)
+    inv_k0 <- 1 / K0
+    object@inverse_reduced_mobility <- inv_k0
+    invisible(object)
+  }
+)