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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
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Error in TreeLine #82

Open anugos opened 2 years ago

anugos commented 2 years ago

Hi Can you plase help me identify the error given below: Error in TreeLine(myDistMatrix = dist, method = "UPGMA", type = "both", : could not find function "TreeLine"

I only have forward reads and have used following command

my_aligned_contigs <- SangerAlignment(ABIF_Directory = "C:/Users/path*1", processMethod = "REGEX", REGEX_SuffixForward = "[0-9]_F.ab1$", REGEX_SuffixReverse = "X.ccc$",minReadsNum=1,M1TrimmingCutoff=.001)

Thank you. -Anu

Kuanhao-Chao commented 2 years ago

Hi @anugos,

In the latest DECIPHER package, the IdCluster() is replaced by TreeLine() function, and the TreeLine() is called inside the SangerAlignment() function that you are running. Since your error message shows that TreeLine() function cannot be found, I would suggest you to update the DECIPHER package to the newest version and try it again. Thanks!

IdClusters(dist,
   type = "both", showPlot = FALSE, processors = processorsNum, verbose = FALSE)

Has been replaced by:

TreeLine(myDistMatrix=dist, method="UPGMA",
   type = "both", showPlot = FALSE, processors = processorsNum, verbose = FALSE)

Best wishes, Kuan-Hao

babinecha commented 2 years ago

I'm having the same issue. How can I update the DECIPHER package? Can you explain?