copyCat

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Error in model.frame.default(...)

4

Dear Chris, I am trying to run the copyCat in the paired mode as follows. ``` copyCat::runPairedSampleAnalysis( annotationDirectory="./annotations/", outputDirectory="./results/", normal="./data/10A_depth.regions.bed", tumor="./data/01A_depth.regions.bed", inputType="bins", readLength=100, maxCores=2, binSize=0, perLibrary=1, perReadLength=0, verbose=TRUE, minMapability=0.6, dumpBins=TRUE,...

eafyounian

Error in { : task 1 failed - "cannot open the connection"

2

When I use copyCat. I met this error: Using copyCat version 1.6.12 [1] "inferred bin size: 10000" [1] "calculating mapability content for read length 100 Fri Oct 22 14:59:56 2021"...

Li-Rui091

Normalization in Chr X and Y

3

Can you please let me know how the normalization happens in specific to sex chromosomes and if it is any different from the autosomal chromosomes? Also, why are you taking...

Viggy0205

Error in hist.default(

11

I use samtools and bcftools call SNVs of tumor and normal bam, and got the VCF file for earch sample when running copyCat I meet this error [1] "inferred that...

zhaoming159753

Suggestion for warning if invalid annotation directory is passed

2

If an incorrect annotation dir is given the `getAnnoDir()` function will first attempt to see if an ideal directory exist, if it doesn't it will look for additional directories `annodir/readlength.*`...

zlskidmore

error in function runPairedSampleAnalysis()

1

Hello, I have tried the copyCat and function runPairedSampleAnalysis() for CNV analysis but got below error. [1] "inferred bin size: 10000" [1] "Can't infer read length from window file headers"...

lida-R