User: twtoal

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twtoal0
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Posts by twtoal

<prev • 59 results • page 1 of 6 • next >
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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 3 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 5 months ago by twtoal0 • updated 5 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 5 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 5 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 5 months ago by twtoal0 • updated 5 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 5 months ago by twtoal0
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Mutation Burden file and manual curation
... Is the mutation burden file produced by Dx.R affected at all by the purity/ploidy selection in the manual curation .csv file?   ...
purecn mutation_burden manual_curation written 5 months ago by twtoal0
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PureCN Solution Heatmap values
... I have a case where the heatmap of PureCN optimal purity/ploidy solutions for a sample shows the maximum likelihood solution (marked with a 1 on the heatmap) is located at what appears to NOT be a heatmap peak.  I examined the heatmap numbers (used PureCN:::.matrixTotalPloidyToTumorPloidy() to get t ...
heatmap purecn likelihoods written 5 months ago by twtoal0
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Comment: C: CNV in Normal Samples?
... Ok.  It would be very nice to be able to use PureCN for the germline too, for consistency's sake if nothing else.  Leaving the normal out of the pool would require making a separate pool file for each normal.  It would be nice if there were a way to tell PureCN to ignore a particular sample in the p ...
written 5 months ago by twtoal0
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CNV in Normal Samples?
... Can PureCN be used to call CNVs in normal germline samples, using the pool of normals database to provide a standard normal reference?   ...
cnv purecn germline normal written 5 months ago by twtoal0 • updated 5 months ago by markus.riester110

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