User: twtoal

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twtoal0
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Posts by twtoal

<prev • 49 results • page 1 of 5 • next >
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PureCN recover optimum solution
... If I edit the manual curation file and change the purity and ploidy, is there any way to later on revert it back to the original PureCN-chosen solution's purity and ploidy (assuming I don't have a record of what that original purity and ploidy were)? Would this be correct?: > res = readRDS(samp ...
purecn optimum_solution written 27 days ago by twtoal0 • updated 27 days ago by markus.riester110
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PureCN PureCN.R --rds option recreate all output files?
... If I've run PureCN once and generated output files including .rds file, if I run it again and specify the --rds argument and give it the name of the .rds file it created in the first run, (and otherwise give it all the same arguments as in the first run), will it re-create all of the output files it ...
purecn --rds written 27 days ago by twtoal0 • updated 27 days ago by markus.riester110
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Comment: C: PureCN Manual Curation .rds file
... Regarding 2, do I need to save a new copy of the original .rds file, i.e. like 3 but instead of using a new file name, just use the original .rds name?  Or, will PureCN itself take care of changing the .rds file when I do 2?   ...
written 28 days ago by twtoal0
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PureCN Manual Curation .rds file
... After performing manual curation (i.e. after creating the manual curation .csv files and editing them to modify the purity and/or ploidy), in order to re-run PureCN.R, which one of these is necessary? 1. Just run PureCN.R the same as before, it will recognize the existence of the curation file and ...
purecn rds_file manual_curation written 28 days ago by twtoal0 • updated 28 days ago by markus.riester110
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Comment: C: Is mean adjusted for purity?
... I think I'll go ahead and open an issue on the PureCN github project for this.   ...
written 28 days ago by twtoal0
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Comment: C: PureCN optimum solution vs heat map
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written 28 days ago by twtoal0
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Comment: C: PureCN optimum solution vs heat map
... Here's an example where I was surprised not to see a solution near (0.2, 2) or (0.25, 3). I also discovered that when I do manual curation, it finds the preselected solution that is closest to the manual curation data I put in, rather than doing a complete recalculation using that data, which surpr ...
written 4 weeks ago by twtoal0
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PureCN optimum solution vs heat map
... Why are the solutions chosen by PureCN and displayed via plotAbs(, type="overview") often located not on the red hotspots of the heatmap, and some hotspots don't have solutions at them?   ...
heatmap purecn solution written 4 weeks ago by twtoal0 • updated 4 weeks ago by markus.riester110
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Answer: A: PureCN: Error in plot.window(...) : need finite 'ylim' values
... I fixed the problem.  There were problems in the VCF files.   ...
written 5 weeks ago by twtoal0
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Comment: C: PureCN: Error in plot.window(...) : need finite 'ylim' values
... Could PureCN be getting some NA values somehow for plotting, and accidentally generating an NA value for ylim?   ...
written 12 weeks ago by twtoal0

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