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README.md

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README

R scripts that were used to make figures for the CA04 methods paper

Contents

  1. Figure_2_coverage_and_quality_scores.R - generates plots of average genome coverage and average quality scores

  2. Figure_3_DNA_copies_impact_sensitivity.R - generates plots shown in panels a and b in Figure 3

  3. Figure_3b_ROC_analyes.R - calculates sensitivity and specificity and generates plot shown in Figure 3d.

  4. Figure_4_SNP_frequency_estimates_depend_on_input_copies.R - generates all the figures shown in figure 4.

  5. Figure_5_coverage_normalization.R - generates comparisons between SNP frequencies called using original vs. normalized data. Also calculates the paired t-tests and R^2 values.

  6. Figure_6_duplicate_removal.R - generates all figures shown in figure 6.

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