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dms-vep / LASV_Josiah_GP_DMS

Analysis of DMS data on Lassa virus GP using dms-vep-pipeline-3
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Additional analyses for revisions #10

Closed Caleb-Carr closed 1 month ago

Caleb-Carr commented 1 month ago

The following additional analyses will be carried out to address reviewers comments:

  1. Create a correlation plot for functional effects measured in 293T cells between library A and library B after averaging each of the four technical replicates in each library. Default correlation plots from pipeline show the individual technical replicate correlations.

  2. Create a correlation plot for single mutant variant scores and the deconvolved single mutant functional effects inferred from the global epistasis model.

  3. Make plots of the distribution of effects of: all amino-acid mutations, amino acid mutations observed at least once in a natural GPC, and amino acids mutations observed at least N times in a natural GPC, where you make some reasonable choice of N > 1 (maybe N = 5?)

  4. Compare DMS scores for each region as defined in Figure 2C to the natural variability (i.e., effective amino acids) for that region (potentially averaged across all sites for a region?)

Caleb-Carr commented 1 month ago

Closing issue to split each point above into its own separate issue