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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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PON - unable to find an inherited method for function ‘seqinfo’ for signature ‘"data.table"’ #110

Open EvoMedLab opened 2 years ago

EvoMedLab commented 2 years ago

I am trying to create a panel of normals from 8 samples, but execution halts. I have checked the input wig files and they appear correct:

Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘seqinfo’ for signature ‘"data.table"’ Calls: loadReadCountsFromWig ... seqlevelsStyle<- -> seqlevelsStyle<- -> seqinfo -> Execution halted

EvoMedLab commented 2 years ago

I confirmed that I receive this error, even when comparing a tumor-normal pair

Correcting Tumour Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘seqinfo’ for signature ‘"data.table"’ Calls: loadReadCountsFromWig ... seqlevelsStyle<- -> seqlevelsStyle<- -> seqinfo ->

Kange2014 commented 1 year ago

Check the version you are using. Pls. make sure u are using the script of the cloned version from the github.