Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
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unable to find an inherited method for function ‘seqinfo’ for signature ‘"RangedData"’ #129
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heweihuang closed 5 months ago
Hi, When running runIchorCNA.R, the following error occurs, my R version is 4.1.3
Parsing: fixedStep chrom=chrX start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=chrY start=1 step=1000000 span=1000000 Sorting by decreasing chromosome size Correcting Tumour Removed 114 bins near centromeres. Applying filter on data... Correcting for GC bias... Correcting for mappability bias... Filtering low uniqueness regions with mappability score < 0.9 Determining gender...Gender unknown Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘seqinfo’ for signature ‘"RangedData"’ Calls: normalizeByPanelOrMatchedNormal ... seqlevelsStyle<- -> seqlevelsStyle<- -> seqinfo ->
In addition: Warning messages:
1: In dir.create(paste0(outDir, "/", id, "/"), recursive = TRUE) :
'./result/out' already exists
2: In regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
collapsing to unique 'x' values
Execution halted