Plotting error

[IanCodes]

I have used conda (v0.3.2 and 0.5.0), and the recommended installation method using R devtools for ichorCNA.
I used the runichorCNA.R script from version 0.3.2, as 0.5.0 on provides an R function in the script.

The script fails at the same place, where it is plotting to a PDF.

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘seqinfo’ for signature ‘"standardGeneric"’
Calls: plotSolutions ... seqlengths -> seqlengths -> seqlengths -> seqinfo -> <Anonymous>

Can anyone tell me the problem here? Thank you.

[xiucz]

Please check your input file type.

[edceeyuchen]

Please check your input file type.

I met the same problem, what's your means the input file? The input file only .wig, right? Could you give me more detail for this bug? Thank you! Best wish

[xiucz]

@edceeyuchen Hi, can you please use this version https://github.com/GavinHaLab/ichorCNA instead? It seems that the GitHub repository is no longer maintained.

I apologize for any confusion. What I meant is that the chromosome types(UCSC, with "chr" or NCBI, without "chr") ) may not be a perfect match?

It's been a while since I last worked on the issue, and I might have forgotten some details. If you have any other questions, feel free to continue the discussion. ^_^

Best, xiucz

[TomokiMotegi]

This error message suggests that if the "seqinfo" is missing, the function tries to use the "standardGeneric" method instead. This error causes describing "NCBI" on the line "ichorCNA_genomeStyle" in config.yaml.

## load seqinfo 
# seqinfo <- getSeqInfo(genomeBuild, genomeStyle)
if (genomeBuild == "hg19" &  genomeStyle == "UCSC") {
  seqinfo <- readRDS("/restricted/projectnb/camplab/home/tmotegi/Work/231025_iChorCNA_test/ichorCNA/inst/extdata/seqinfo_hg19_ucsc.rds")
}
if (genomeBuild == "hg38" &  genomeStyle == "UCSC") {
  seqinfo <- readRDS("/restricted/projectnb/camplab/home/tmotegi/Work/231025_iChorCNA_test/ichorCNA/inst/extdata/seqinfo_hg38_ucsc.rds")
}