From 3a37275551a20f29f3e56e0e44a451bc9fc043c7 Mon Sep 17 00:00:00 2001
From: Quentin <q.petitjean1@gmail.com>
Date: Tue, 4 Apr 2023 17:35:11 +0200
Subject: [PATCH] Changing frags to track

---
 R/analyseTimeBoots.r | 8 ++++----
 R/convert2frags.R    | 2 +-
 R/convert2list.R     | 2 +-
 R/mirrorYFunc.R      | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/analyseTimeBoots.r b/R/analyseTimeBoots.r
index d3eecd8..5e27469 100644
--- a/R/analyseTimeBoots.r
+++ b/R/analyseTimeBoots.r
@@ -312,7 +312,7 @@ analyseTimeBoots <-
             data.frame(
               Res = Res[[x]],
               len = len[[x]],
-              fragId = names(WhoWhen)
+              trackId = names(WhoWhen)
             ))
         names(Reslen) <- names(Res)
         # create an equivalent of na.rm = T, useful to compute the weighed mean for each metric and
@@ -346,7 +346,7 @@ analyseTimeBoots <-
         }
         # create a list of the fragment that could be sampled for each customfunc (after removing fragments which return NA)
         toSample <- lapply(Reslen, function (x)
-          x$fragId)
+          x$trackId)
         # check the number of fragments that could be sampled for each customfunc (after removing fragments which return NA)
         toSampleLen <- lapply(toSample, length)
         # in case the number of fragments that could be sampled differ among customfunc, identify for which customfunc it is the case
@@ -431,7 +431,7 @@ analyseTimeBoots <-
         bootsamplesVal <-
           lapply(names(bootsamples), function(x) {
             array(unlist(lapply(seq(bootn), function(y) {
-              Reslen[[x]]$Res[match(bootsamples[[x]][, y], Reslen[[x]]$fragId)]
+              Reslen[[x]]$Res[match(bootsamples[[x]][, y], Reslen[[x]]$trackId)]
             })), dim = c(length(bootsamples[[x]]) / bootn, bootn))
           })
         names(bootsamplesVal) <- names(bootsamples)
@@ -439,7 +439,7 @@ analyseTimeBoots <-
         bootsampleslen <-
           lapply(names(bootsamples), function(x) {
             array(unlist(lapply(seq(bootn), function(y) {
-              Reslen[[x]]$len[match(bootsamples[[x]][, y], Reslen[[x]]$fragId)]
+              Reslen[[x]]$len[match(bootsamples[[x]][, y], Reslen[[x]]$trackId)]
             })), dim = c(length(bootsamples[[x]]) / bootn, bootn))
           })
         names(bootsampleslen) <- names(bootsamples)
diff --git a/R/convert2frags.R b/R/convert2frags.R
index 12ea8d4..b265913 100644
--- a/R/convert2frags.R
+++ b/R/convert2frags.R
@@ -32,7 +32,7 @@
 #'trackDatList <- convert2list(fragsList)
 #'
 #'# convert the list of variable to a liost of fragment based on fragments identity
-#'trackDat <- convert2frags(trackDatList, by = "fragsId")
+#'trackDat <- convert2frags(trackDatList, by = "trackId")
 #'
 #' @export
 
diff --git a/R/convert2list.R b/R/convert2list.R
index f614331..c3d5412 100644
--- a/R/convert2list.R
+++ b/R/convert2list.R
@@ -36,7 +36,7 @@
 convert2list <- function(trackDat) {
   # convert the fragments' list to a data frame and add the fragment id
   trackDatdf <- do.call("rbind", trackDat)
-  trackDatdf[["fragsId"]] <-
+  trackDatdf[["trackId"]] <-
     gsub("[.][0-9]*", "", rownames(trackDatdf))
   # then transform the data frame to a list
   trackDatList <- as.list(trackDatdf)
diff --git a/R/mirrorYFunc.R b/R/mirrorYFunc.R
index 5e28ddb..fa014c7 100644
--- a/R/mirrorYFunc.R
+++ b/R/mirrorYFunc.R
@@ -39,7 +39,7 @@
 #'   mirrorYFunc(trackDatList[["y.pos"]], imgHeight = imgHeight)
 #' 
 #' # convert the new dataset to a list of fragment
-#' fragsListMirrored <- convert2frags(trackDatList, by = "frags_id")
+#' fragsListMirrored <- convert2frags(trackDatList, by = "trackId")
 #' 
 #' # draw the result
 #' # here we can see that both trajectory are mirrored, with the original trajectory