fixes

R/AllGenerics.R

@@ -80,10 +80,10 @@ setGeneric("addProcessHistory", function(object, ...)
 #'   example, by checking the number of matches and ranges of the matching
 #'   peaks, by first running `[matchLamasChromPeaks()]`.
 #'
-#'   Different warping methods are available; users can choose to fit a loess
-#'   (`method = "loess"`, the default) or a gam (`method = "gam"`) between the
+#'   Different warping methods are available; users can choose to fit a *loess*
+#'   (`method = "loess"`, the default) or a *gam* (`method = "gam"`) between the
 #'   reference data points and observed matching ChromPeaks. Additional
-#'   parameters such as `span`, `weight`, `outlier_tolerance`, `zeroWeight`,
+#'   parameters such as `span`, `weight`, `outlierTolerance`, `zeroWeight`,
 #'   and `bs` are specific to these models. These parameters offer flexibility
 #'   in fine-tuning how the matching chromatographic peaks are fitted to the
 #'   lamas, thereby generating a model to align the overall retention time for

R/do_adjustRtime-functions.R

@@ -741,13 +741,13 @@ adjustRtimeSubset <- function(rtraw, rtadj, subset,
 #' @title Match reference Lamas to ChromPeaks for evaluation prior to alignment
 #'
 #' @description
-#' This function quickly matches each file's ChromPeaks to Lamas, allowing the
-#' user to evaluate the matches for each file.
+#' The `matchLamasChromPeaks()` function quickly matches each file's ChromPeaks
+#' to Lamas, allowing the user to evaluate the matches for each file.
 #'
 #' @param object An object of class `XcmsExperiment` with defined ChromPeaks.
 #'
 #' @param param An object of class `LamaParama` that will later be used for
-#' adjustment using the [adjustRtime()] function.
+#' adjustment using the `[adjustRtime()]` function.
 #'
 #' @return A `LamaParama` object with new slot rtMap composed of a list of
 #' matrices representing the 1:1 matches between Lamas (ref) and ChromPeaks
@@ -757,7 +757,7 @@ adjustRtimeSubset <- function(rtraw, rtadj, subset,
 #' calling [adjustRtime()] with the same `LamaParama` and `XcmsExperiment`
 #' object.
 #'
-#' @author Philippine Louail
+#' @author Philippine Louail, Carl Brunius
 #'
 #' @rdname matchLamaChromPeaks
 matchLamasChromPeaks <- function(object, param, BPPARAM = bpparam()){
@@ -778,18 +778,23 @@ matchLamasChromPeaks <- function(object, param, BPPARAM = bpparam()){
 #' @title Summary of LamaParama retention time alignment
 #'
 #' @description
-#' Generates a summary of the LamaParama method. Composed of coverage % of the
-#' chrompeaks match over the total chrompeaks of the object. as well as a
-#' summary of the model that will be applied to the file to adjust the
-#' retention times
+#' The `summarizeLamaMatch()` generates a summary of the LamaParama method.
+#' Composed of coverage % of the chrompeaks match over the total chrompeaks of
+#' the object. as well as a summary of the model that will be applied to the
+#' file to adjust the retention times
 #'
 #' @param `LamaParama` same object that will be passed to the `adjustRtime()`
 #' function. To run this function the `matchLamasChromPeaks()` need to be run
 #' on this first.
 #'
-#' @return a data.frame
+#' @return A `data.frame` with:
 #'
-#' @author Philippine Louail
+#' - Total_peaks: total number of chromatographic peaks in the file
+#' - Matched_peak: The number of matched peaks to Lamas
+#' - Total_Lamas: Total number of Lamas
+#' - Model_summary: `summary.loess` or `summary.gam` object for each file.
+#'
+#' @author Philippine Louail, Carl Brunius
 #'
 #' @rdname matchLamaChromPeaks
 summarizeLamaMatch <- function(param){
@@ -808,7 +813,7 @@ summarizeLamaMatch <- function(param){
                       zero_weight = param@zeroWeight,
                       bs = param@bs))
         })
-    res$model_summary <- res_model
+    res$Model_summary <- res_model
     res
 }
 

R/functions-Params.R

@@ -313,8 +313,8 @@ LamaParama <- function(lamas = matrix(ncol = 2, nrow = 0,
 #' @export
 #'
 #' @rdname matchLamaChromPeaks
-rtMap <- function(x){
-    if(!inherits(x, "LamaParama"))
+rtMap <- function(param){
+    if(!inherits(param, "LamaParama"))
         stop("The inputs need to be of class LamaParama")
     rtMap <- param@rtMap
     rtMap

inst/NEWS

@@ -4,9 +4,9 @@ Changes in version 4.1.10
 - Implementation of the `LamaParama` class and method for the `adjustRtime()`
  function. Allowing alignment of a dataset based on landmarks (lamas) from an
  external reference dataset.
-- Implementation of related user-level function `matchLamasChromPeaks()` which
-  allows  for pre evaluation of matching between lamas and chromPeaks before
-  alignment.
+- Implementation of related user-level function `matchLamasChromPeaks()`,
+  `summarizeMatchLama()` and `plot(LamaParama)` which allows for evaluation of
+  matching between lamas and chromPeaks.
 
 Changes in version 4.1.9
 ----------------------

tests/testthat/test_do_adjustRtime-functions.R

@@ -390,7 +390,7 @@ test_that("summarizeLamaMatch works", {
     res <- summarizeLamaMatch(param)
     expect_equal(nrow(res), length(tst))
     expect_equal(ncol(res), 4)
-    expect_true(inherits(res$model_summary[[1]], "summary.loess"))
+    expect_true(inherits(res$Model_summary[[1]], "summary.loess"))
 })
 
 test_that("Accessing rtMap from LamaParama object works", {

vignettes/xcms.Rmd

@@ -1410,6 +1410,9 @@ chromatographic peaks along with the fitted model line.
 summary <- summarizeLamaMatch(param)
 summary 
 
+# coverage for each file
+summary$Matched_peaks / summary$Total_peaks * 100
+
 #access the information on the model of for the first file 
 summary$model_summary[[1]]