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make a scan plotting function? #5

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rcorty opened this issue Mar 6, 2019 · 2 comments
Open

make a scan plotting function? #5

rcorty opened this issue Mar 6, 2019 · 2 comments
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core a core function of vqtl2 enhancement New feature or request
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@rcorty
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rcorty commented Mar 6, 2019

or maybe continue to use functions from qtl

@rcorty rcorty added the enhancement New feature or request label Mar 7, 2019
@rcorty rcorty added the core a core function of vqtl2 label Mar 16, 2019
@rcorty
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rcorty commented Mar 19, 2019

As discussed with @gkeele, there are some decisions to make about what to plot when the model did not converge at a specific locus

  • nothing at that locus (i.e. discontinuity in geom_line)
  • linear interpolation between nearest loci where we do have a test statistica availble

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rcorty commented Mar 21, 2019

done in bb17f7d

currently plotting LR at each locus and interpolating linearly over NA's

next steps will be to give the user options on what to plot -- LR vs. LOD vs. single-locus-p-value (chisq test on LR)

next next steps will rely on having permutations set up so that we can compute and then plot p-values that correct for multiple comparisons

@rcorty rcorty added this to the version 2.0 milestone Mar 21, 2019
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Labels
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