Error in TreeLine

[anugos]

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]

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Has been replaced by: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]

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