EXCAVATOR2 problems: CorrectSize function? · Biostar

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EXCAVATOR2 problems: CorrectSize function?

Hi, I am wondering if anyone has experience in successfully running EXCAVATOR2? I have spent lots of time on it but no luck. Tried to contact the authors with no response so far.

I got stuck in the 2nd step when running "perl EXCAVATORDataPrepare.pl". By checking all the R codes, Perl codes and bash scripts, I found I got stuck at the R script: EXCAVATORNormalizationExome.R, at line 80: "RCLNormListIn <- CorrectSize(RCTL[indInTarget],L[indInTarget],step)". Looks like "CorrectSize" is an R function, but there is no where in the whole package that this function was supplied. I also tried to find this function in all the current R packages but doesn't look like it's there.

I feel like I must have missed something, but just couldn't figure out what I have missed. Any help would be much appreciated.

next-gen sequencing

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updated 9.3 years ago by Biostar

• written 9.4 years ago by joan.chen •

Are you sure that it has been installed successfully in R? Do you have the correct version of R installed?

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written 8.9 years ago by Kevin Blighe

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