Issues with Reproducible tutorial

[jspychalla]

Hello,

I am trying to run the reproducible example from :

When I run the SangerAlignment function below

my_sangerAlignment <- new("SangerAlignment",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = parentDir,
REGEX_SuffixForward = "_[0-9]F.ab1$",
REGEX_SuffixReverse = "[0-9]_R.ab1$",
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
geneticCode = GENETIC_CODE,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 2)

I get the following error message:

Error in IdClusters(dist, type = "both", showPlot = FALSE, processors = processorsNum, :
unused arguments (type = "both", showPlot = FALSE)

This same error appears when I run

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')

ACHLO_contigs <- SangerAlignment(ABIF_Directory = parentDir,
REGEX_SuffixForward = "_[0-9]F.ab1$",
REGEX_SuffixReverse = "[0-9]_R.ab1$")

The version of R I am working in is 4.2.2.

[jspychalla]

I realize that the SangerAlignment function is not present even though I have the package loaded. Is there a way to fix this?
Thank you :)

[Kuanhao-Chao]

Hi @jspychalla,

Please excuse the delay.

DECIPHER changed the IdClusters function to TreeLine. But this issue was solved in 3.15 release. Which version of sangeranalyseR are you using?

Please upgrade it by running

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sangeranalyseR")

And you still cannot load the function, please send me an email to [email protected]

Best,
Kuan-Hao