18 research outputs found
Ghanian sample summary.
<p>The frequency of inferred number of strains per sample (left) and and the panmixia coefficient by number of strains (right). MAP estimates used.</p
Parameters and definitions for the model and its description.
<p>Parameters and definitions for the model and its description.</p
Performance for parameter inference.
<p>Upper row: mean squared deviation for strain frequencies by number of read counts (left) and by number of SNPs (right). Lower row: absolute normalized deviation for panmixia coefficient by number of read counts (left) and by number of SNPs.</p
Examples of real and model-simulated data.
<p>For three samples (rows), we present the observed data WSAF plotted against the PLAF (first column), a diagram of the inferred model indicating the bands, proportions, and panmixia coefficient (second column), and data simulated under the inferred model. Panmixia coefficient and strain proportions are the MAP values. In the second column, the model’s PLAF-varying mixture densities are shown in grey scale, with black equal to one.</p
Number of strains by F-statistic.
<p>Boxplot of the inbreeding coefficient (1 − <i>F</i><sub><i>is</i></sub>) for each sample grouped by the MAP number of inferred strains.</p
Table of simulated parameter values. <i>C</i> is the number of read counts while <i>M</i>, <i>K</i> and <i>α</i> are as in Table 1.
<p>Table of simulated parameter values. <i>C</i> is the number of read counts while <i>M</i>, <i>K</i> and <i>α</i> are as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004824#pcbi.1004824.t001" target="_blank">Table 1</a>.</p
Component inference.
<p><i>Maximum a posteriori</i> (MAP) inferred number of components by number of read counts across 10 simulations, with dotted line at the true number of components.</p
Using BWT structures for reference-free querying of the 1000 Genomes sequence data
<p>Using BWT structures for reference-free querying of<br>the 1000 Genomes sequence data</p>
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Runtime and memory requirements comparison of HLA*PRG, PHLAT and HLAReporter on NA12878.
<p>Upper part: NA12878 2 x 100bp reads from the Platinum cohort; lower part: NA12878 2 x 250bp reads from the 1000 Genomes cohort. We provide a detailed analysis in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005151#pcbi.1005151.s014" target="_blank">S1 Text</a>.</p
HLA type inference accuracy for HLA*PRG and two state-of-the-art algorithms.
<p>HLA type inference accuracy for HLA*PRG and two state-of-the-art algorithms.</p