Dataset Information

High-Order Spatial Simulation Using Legendre-Like Orthogonal Splines.

ABSTRACT: High-order sequential simulation techniques for complex non-Gaussian spatially distributed variables have been developed over the last few years. The high-order simulation approach does not require any transformation of initial data and makes no assumptions about any probability distribution function, while it introduces complex spatial relations to the simulated realizations via high-order spatial statistics. This paper presents a new extension where a conditional probability density function (cpdf) is approximated using Legendre-like orthogonal splines. The coefficients of spline approximation are estimated using high-order spatial statistics inferred from the available sample data, additionally complemented by a training image. The advantages of using orthogonal splines with respect to the previously used Legendre polynomials include their ability to better approximate a multidimensional probability density function, reproduce the high-order spatial statistics, and provide a generalization of high-order simulations using Legendre polynomials. The performance of the new method is first tested with a completely known image and compared to both the high-order simulation approach using Legendre polynomials and the conventional sequential Gaussian simulation method. Then, an application in a gold deposit demonstrates the advantages of the proposed method in terms of the reproduction of histograms, variograms, and high-order spatial statistics, including connectivity measures. The C++ course code of the high-order simulation implementation presented herein, along with an example demonstrating its utilization, are provided online as supplementary material.

SUBMITTER: Minniakhmetov I

PROVIDER: S-EPMC6411132 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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High-Order Spatial Simulation Using Legendre-Like Orthogonal Splines.

Minniakhmetov Ilnur I Dimitrakopoulos Roussos R Godoy Marcelo M

Mathematical geosciences 20180517 7

High-order sequential simulation techniques for complex non-Gaussian spatially distributed variables have been developed over the last few years. The high-order simulation approach does not require any transformation of initial data and makes no assumptions about any probability distribution function, while it introduces complex spatial relations to the simulated realizations via high-order spatial statistics. This paper presents a new extension where a conditional probability density function ( ...[more]

PMID: 30931017

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Project description:BackgroundNext-generation sequencing has been used by investigators to address a diverse range of biological problems through, for example, polymorphism and mutation discovery and microRNA profiling. However, compared to conventional sequencing, the error rates for next-generation sequencing are often higher, which impacts the downstream genomic analysis. Recently, Wang et al. (BMC Bioinformatics 13:185, 2012) proposed a shadow regression approach to estimate the error rates for next-generation sequencing data based on the assumption of a linear relationship between the number of reads sequenced and the number of reads containing errors (denoted as shadows). However, this linear read-shadow relationship may not be appropriate for all types of sequence data. Therefore, it is necessary to estimate the error rates in a more reliable way without assuming linearity. We proposed an empirical error rate estimation approach that employs cubic and robust smoothing splines to model the relationship between the number of reads sequenced and the number of shadows.ResultsWe performed simulation studies using a frequency-based approach to generate the read and shadow counts directly, which can mimic the real sequence counts data structure. Using simulation, we investigated the performance of the proposed approach and compared it to that of shadow linear regression. The proposed approach provided more accurate error rate estimations than the shadow linear regression approach for all the scenarios tested. We also applied the proposed approach to assess the error rates for the sequence data from the MicroArray Quality Control project, a mutation screening study, the Encyclopedia of DNA Elements project, and bacteriophage PhiX DNA samples.ConclusionsThe proposed empirical error rate estimation approach does not assume a linear relationship between the error-free read and shadow counts and provides more accurate estimations of error rates for next-generation, short-read sequencing data.

Dataset Information

High-Order Spatial Simulation Using Legendre-Like Orthogonal Splines.

Publications

High-Order Spatial Simulation Using Legendre-Like Orthogonal Splines.

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