Author: Palmer, Duncan S.; Turner, Isaac; Fidler, Sarah; Frater, John; Goedhals, Dominique; Goulder, Philip; Huang, Kuan-Hsiang Gary; Oxenius, Annette; Phillips, Rodney; Shapiro, Roger; Vuuren, Cloete van; McLean, Angela R.; McVean, Gil
Title: Mapping the drivers of within-host pathogen evolution using massive data sets Document date: 2019_7_9
ID: 100r7w2n_67
Snippet: Using each of the five methods described above, plus our new approach as described in detail in the methods section of the main text, we obtain p-values or parameter estimates which provide a metric for the strength of selection for escape at each site, conditional on each of the HLA types. We use the p-value, p-value, escape rate estimate, probability estimate, strength of selection; a i , and median HLA associated selection parameters; γ h for.....
Document: Using each of the five methods described above, plus our new approach as described in detail in the methods section of the main text, we obtain p-values or parameter estimates which provide a metric for the strength of selection for escape at each site, conditional on each of the HLA types. We use the p-value, p-value, escape rate estimate, probability estimate, strength of selection; a i , and median HLA associated selection parameters; γ h for each of the six methods respectively to determine ROC curves for each of the 100 simulated sequence and host HLA data sets, displayed in Figure 2 of the main text. We also examined the effect of increasing the query sequence set with associated host HLA information to 3000. The resultant ROC curves for each of the five methods are shown in Supplementary Figure 7 .
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