fix inconsitency bugs

lerch-a · Dec 19, 2024 · 9f842b7 · 9f842b7
1 parent 0b104de
commit 9f842b7
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/R/minION_function.R b/R/minION_function.R
@@ -45,6 +45,9 @@ demultiplexByMarkerMinION <- function (sampleTable, markerTable, outputDir, trim
   }))
   resM <- merge.data.frame(sampleTable[, c("SampleID", "SampleName", 
                                            "BarcodePair")], resM, by = c("SampleID", "BarcodePair"))
+  # temporary fix of historical issues
+  sampleTable$ReadFile <- sampleTable$FileR1
+  sampleTable$FileR1 <- NULL
   return(resM)
 }
 

diff --git a/docs/documentation/minIonDR_workflow.md b/docs/documentation/minIonDR_workflow.md
@@ -20,7 +20,7 @@ To install HaplotypR start R and first install ShortRead and dada2 by typing:
 ```R
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install(c("ShortRead","dada2")
+BiocManager::install(c("ShortRead","dada2"))
 ```
 
 Then install devtools by typing
@@ -116,11 +116,9 @@ write.csv(finalTab, file=file.path(outputDir, "finalHaplotypList_vMinION.csv"),
 
 Calculate mismatch rate and call SNPs
 ```R
-dePlexMarker <- dePlexMarker[dePlexMarker$]
-
 refSeq <- DNAStringSet(markerTab$ReferenceSequence)
 names(refSeq) <- markerTab$MarkerID
-snpLst <- createSNPsList(outputDir, sampleTable=dePlexMarker, markerTable=markerTab, refSeq=refSeq, postfix=postfix)
+snpLst <- createSNPsList(outputDir, sampleTable=dePlexMarker, markerTable=markerTab, refSeq=refSeq)
 ```
 
 

diff --git a/docs/documentation/minIon_workflow.md b/docs/documentation/minIon_workflow.md
@@ -20,7 +20,7 @@ To install HaplotypR start R and first install ShortRead and dada2 by typing:
 ```R
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install(c("ShortRead","dada2")
+BiocManager::install(c("ShortRead","dada2"))
 ```
 
 Then install devtools by typing