darrenabbey
commented
7 years ago Some terminology may need to be clarified. "Baseline Ploidy" as originally written is used in figure generation only, while "Experimental Ploidy" (I forget exact use. I'll have to check later) is used to scale normalized CNV data and thus determine theoretical SNP ratio peaks.
On Sep 27, 2016 8:49 AM, "Vladimir Gritsenko" notifications@github.com wrote:
Today, in order to correctly assign the allelic ratios (and assign colors in the SNP diagrams created with a hapmap) the user needs to provide the correct baseline ploidy. This tells Ymap which possible ratios the SNPs can fall into. For example, in a diploid segment, the only possible SNP ratios are 2:0, 1:1, and 0:2. However, if the segment is triploid, then the actual ratios are 3:0, 2:1, 1:2 and 0:3. Only the homozygotes can be correctly assigned a color, and the rest will be either strictly incorrect or appeared smeared.
Many times the user can only guess the baseline ploidy, and sometimes they even incorrectly assume it, and don't look at the allele ratio diagrams to re-run the dataset. So it may be a good idea to introduce an automatic detection of the baseline ploidy.
The working suggestion is this: take all segments with CNV matching the baseline ploidy. Find the peaks of the allele ratios within them. Match the ratios those peaks represent with a ploidy, and use that as the baseline ploidy in the rest of the analysis. So, for example, if we see a peak at 0 and a peak at 0.75, we can assume that the baseline ploidy is 4 (this was actually observed in a strain assumed to be haploid).
@darrenabbey https://github.com/darrenabbey , what do you think?
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vladimirg
Today, in order to correctly assign the allelic ratios (and assign colors in the SNP diagrams created with a hapmap) the user needs to provide the correct baseline ploidy. This tells Ymap which possible ratios the SNPs can fall into. For example, in a diploid segment, the only possible SNP ratios are 2:0, 1:1, and 0:2. However, if the segment is triploid, then the actual ratios are 3:0, 2:1, 1:2 and 0:3. Only the homozygotes can be correctly assigned a color, and the rest will be either strictly incorrect or appeared smeared.
Many times the user can only guess the baseline ploidy, and sometimes they even incorrectly assume it, and don't look at the allele ratio diagrams to re-run the dataset. So it may be a good idea to introduce an automatic detection of the baseline ploidy.
The working suggestion is this: take all segments with CNV matching the baseline ploidy. Find the peaks of the allele ratios within them. Match the ratios those peaks represent with a ploidy, and use that as the baseline ploidy in the rest of the analysis. So, for example, if we see a peak at 0 and a peak at 0.75, we can assume that the baseline ploidy is 4 (this was actually observed in a strain assumed to be haploid).
@darrenabbey , what do you think?