Goals
• Reproduce
• Similar behavior in other genes/samples?
• Do simulated reads predict observed
data? Get a measure by gene
• Even more than by chance?
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Original
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Reproduced
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Measures by gene: using single bp exon
• Correlation (R^2)
• RMSD: scaling by max first
• ARIMA: forecast models
– Auto ARIMA on obs
– Fit again using simulated data as predictor
– P-value for predictor and estimated coef
• Chance:
– Neg. binomial size 1 and 6
– Compare replicates of simulated data
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• d: default params, 2 reps (2x)
• r: using rnaf bias, 2x
• b1: neg. binomial with size = 1, 2x
• b6: neg. binom. size = 6, 2x
• d1-d2: using d1 as “obs”
– Same for r1-r2, b1a-b1b, b6a-b6b
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Correlation
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Correlation: summarize by sample
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Correlation: summarize by gene
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R^2
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Scaling by max then RMSD
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Scaling by max then RMSD
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ARIMA: predictor p-value
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ARIMA: predictor p-value
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ARIMA: predictor coefficient
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Code
• https://github.com/alyssafrazee/polyest
er_code/blob/master/polyester_manuscri
pt.Rmd
• https://github.com/lcolladotor/mapBias
(private for now)