User: twtoal

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twtoal0
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Posts by twtoal

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Comment: C: callLOH output file NA values
... It looks like the keep.no.snp.segments = FALSE argument to callLOH() has no equivalent option argument in PureCN.R ? ...
written 6 months ago by twtoal0
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Comment: C: callLOH output file NA values
... Ok, thanks. It didn't occur to me that that change might introduce NAs in result. Since I don't call callLOH() directly, but use PureCN.R to do it for me, I'm not real tuned in to those function names. What might be helpful is to mention output filenames in the release notes, e.g.: ``` callLOH ( ...
written 6 months ago by twtoal0
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callLOH output file NA values
... I updated to a newer version of PureCN and ran into a problem in my post-processing of PureCN output from callLOH. The problem was caused by NA values in the "M" column. My previous PureCN version never had NA values in the column. The PureCN doc file doesn't mention NA in its description of the ...
purecn na values written 6 months ago by twtoal0 • updated 6 months ago by markus.riester110
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PureCN.R warning "duplicate keys in header will be forced to unique rownames"
... Running PureCN.R v 1.13.21, I get this warning and these "null device" messages. Are they something to be concerned about? ``` ...snip... INFO [2019-04-29 15:42:06] Fitting variants for purity 0.37, tumor ploidy 3.73 and contamination 0.01. Warning message: In .bcfHeaderAsSimpleList(header) : du ...
purecn written 6 months ago by twtoal0 • updated 6 months ago by markus.riester110
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Chromosome arm loss and --maxhomozygousloss default
... I see that the default value for the PureCN.R --maxhomozygousloss option is 0.05,1e+07.  Does this mean that if entire chromosome arms are lost, they must not total more than 5% of the genome?     ...
purecn maxhomozygousloss written 11 months ago by twtoal0
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Copy ratio close to but not exactly 1
... In my PureCN results I see with most samples that there will be long stretches of the genome, e.g. many separate chromosomes, where the copy ratio (2 ^ log ratio) is approximately but not exactly 1, such as for example 1.02, 1.03, 0.98.  Typically the number is consistent in any given sample, perhap ...
purecn copyratio written 13 months ago by twtoal0 • updated 13 months ago by markus.riester110
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Comment: C: Assigning DUP/DEL p-value to CNV segment
... Sorry, my edit to my question crossed with your response, can you re-read my question and adjust your response? ...
written 13 months ago by twtoal0
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Assigning DUP/DEL p-value to CNV segment
... Does the following seem like a good method to assign a p-value for segment DUPLICATION or DELETION, to each segment in the dnacopy.seg file? 1. Use PureCN's readCurationFile to read the .rds file into object RDS, then retrieve the log ratios of the marks in RDS$input$log.ratio 2. Compute the adjus ...
purecn written 13 months ago by twtoal0
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Copy ratio threshold for calling actual CNV
... What would you recommend regarding how to choose two thresholds (LO, HI) for adjusted copy ratio (CR), such that CR < LO is called a deletion and CR > HI is called a duplication?   ...
purecn threshold copy-ratio written 13 months ago by twtoal0 • updated 13 months ago by markus.riester110
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Answer: A: Mutation Burden file and manual curation
... Okay, I'm just working on some reorganization to my pipeline.  I've decided to duplicate all the PureCN.R output files, one set prior to manual curation and the second after it.  I think I'll run Dx.R on the manually curated output, no need to run it on the initial output.   ...
written 13 months ago by twtoal0

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