2022
DOI: 10.1093/gbe/evac047
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Correcting Bias in Allele Frequency Estimates Due to an Observation Threshold: A Markov Chain Analysis

Abstract: There are many problems in biology and related disciplines involving stochasticity, where a signal can only be detected when it lies above a threshold level, while signals lying below threshold are simply not detected. A consequence is that the detected signal is conditioned to lie above threshold, and is not representative of the actual signal. In this work we present some general results for the conditioning that occurs due to the existence of such an observational threshold. We show that this conditioning i… Show more

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Cited by 2 publications
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“…Significant differences were nonetheless observed based on the proportion of contamination, feature type and application of deconvolution (F=33.04; p<10 -6 ; R 2 =0.583). Generally, specificity increased with increasing levels of contamination (F=23.03; p=3.22x10 -6 ; Partial-R 2 =0.561)—likely due to lower depth and power (Gossmann & Waxman, 2022). Specificity differed by feature type (F=20.6; p<10 -6 ; Partial-R 2 =0.465), with large features—excluding comparisons between non-CpG methylation and CpG islands—showing somewhat lower specificity than single sites (Tukey Honest Significant Differences Post-Hoc: p<10 -5 ).…”
Section: Resultsmentioning
confidence: 99%
“…Significant differences were nonetheless observed based on the proportion of contamination, feature type and application of deconvolution (F=33.04; p<10 -6 ; R 2 =0.583). Generally, specificity increased with increasing levels of contamination (F=23.03; p=3.22x10 -6 ; Partial-R 2 =0.561)—likely due to lower depth and power (Gossmann & Waxman, 2022). Specificity differed by feature type (F=20.6; p<10 -6 ; Partial-R 2 =0.465), with large features—excluding comparisons between non-CpG methylation and CpG islands—showing somewhat lower specificity than single sites (Tukey Honest Significant Differences Post-Hoc: p<10 -5 ).…”
Section: Resultsmentioning
confidence: 99%