Bayesian diagnostic analysis for quantitative trait loci mapping

2019 ◽  
Vol 29 (8) ◽  
pp. 2238-2249
Author(s):  
Daiane A Zuanetti ◽  
Júlia M Pavan Soler ◽  
José E Krieger ◽  
Luis A Milan

QTL mapping is an important tool for identifying regions in chromosomes which are relevant to explain a response of interest. It is a special case of the regression model where an unknown number of missing (non-observable) covariates is involved leading to a complex variable selection procedure. Although several methods have been proposed to identify QTLs and to estimate parameters in the associated model, minimum attention has been devoted to the estimated model adequacy. In this paper, we present an overview of a few methods for residual and diagnostic analysis in the context of Bayesian regression modeling and adapt them to work with QTL mapping. The motivation of this study is to identify QTLs associated with the blood pressure of F2 rats and check the fitted model adequacy.

2018 ◽  
Vol 8 (2) ◽  
pp. 313-341
Author(s):  
Jiajie Chen ◽  
Anthony Hou ◽  
Thomas Y Hou

Abstract In Barber & Candès (2015, Ann. Statist., 43, 2055–2085), the authors introduced a new variable selection procedure called the knockoff filter to control the false discovery rate (FDR) and proved that this method achieves exact FDR control. Inspired by the work by Barber & Candès (2015, Ann. Statist., 43, 2055–2085), we propose a pseudo knockoff filter that inherits some advantages of the original knockoff filter and has more flexibility in constructing its knockoff matrix. Moreover, we perform a number of numerical experiments that seem to suggest that the pseudo knockoff filter with the half Lasso statistic has FDR control and offers more power than the original knockoff filter with the Lasso Path or the half Lasso statistic for the numerical examples that we consider in this paper. Although we cannot establish rigourous FDR control for the pseudo knockoff filter, we provide some partial analysis of the pseudo knockoff filter with the half Lasso statistic and establish a uniform false discovery proportion bound and an expectation inequality.


2020 ◽  
Vol 12 (10) ◽  
pp. 1637 ◽  
Author(s):  
Le Bienfaiteur T. Sagang ◽  
Pierre Ploton ◽  
Bonaventure Sonké ◽  
Hervé Poilvé ◽  
Pierre Couteron ◽  
...  

Precise accounting of carbon stocks and fluxes in tropical vegetation using remote sensing approaches remains a challenging exercise, as both signal saturation and ground sampling limitations contribute to inaccurate extrapolations. Airborne LiDAR Scanning (ALS) data can be used as an intermediate level to radically increase sampling and enhance model calibration. Here we tested the potential of using ALS data for upscaling vegetation aboveground biomass (AGB) from field plots to a forest-savanna transitional landscape in the Guineo–Congolian region in Cameroon, using either a design-based approach or a model-based approach leveraging multispectral satellite imagery. Two sets of reference data were used: (1) AGB values collected from 62 0.16-ha plots distributed both in forests and savannas; and (2) an AGB map generated form ALS data. In the model-based approach, we trained Random Forest models using predictors from recent sensors of varying spectral and spatial resolutions (Spot 6/7, Landsat 8, and Sentinel 2), along with biophysical predictors derived after pre-processing into the Overland processing chain, following a forward variable selection procedure with a spatial 4-folds cross validation. The models calibrated with field plots lead to a systematic overestimation in AGB density estimates and a root mean squared prediction error (RMSPE) of up to 65 Mg.ha−1 (90%), whereas calibration with ALS lead to low bias and a drop of ~30% in RMSPE (down to 43 Mg.ha−1, 58%) with little effect of the satellite sensor used. Decomposing bias along the AGB density range, we show that multispectral images can (in some specific cases) be used for unbiased prediction at landscape scale on the basis of ALS-calibrated statistical models. However, our results also confirm that, whatever the spectral indices used and attention paid to sensor quality and pre-processing, the signal is not sufficient to warrant accurate pixelwise predictions, because of large relative RMSPE, especially above (200–250 t/ha). The design-based approach, for which average AGB density values were attributed to mapped land cover classes, proved to be a simple and reliable alternative (for landscape to region level estimations), when trained with dense ALS samples.


1958 ◽  
Vol 195 (2) ◽  
pp. 362-368 ◽  
Author(s):  
J. Stamler ◽  
L. Dreifus ◽  
L. N. Katz ◽  
I. J. Lichton

In Ringer's-infused unanesthetized intact dogs, rapid intravascular injections (200 cc) caused an enhanced diuresis, regardless of injection site. Injection of Ringer's solution induced an immediate and sustained increment of H2O, Na and total solute diuresis. These changes were correlated with increases in venous pressure, reductions in hematocrit and in plasma oncotic pressure (except in the dextran experiments). They were not correlated with patterns of GFR, RPF, plasma Na and total solute, filtered electrolyte load, blood pressure of heart rate. Injection of 3.75% glucose-in-water induced a sustained increment of H2O diuresis, with only a transient or no increase in Na and total solute diuresis. Injection of 6% dextran-in-water induced a complex, variable response, with sustained enhanced diuresis of H2O, Na and total solutes in some experiments. It is suggested that two adjustments, volume and composition homeostatic correction, are operative, the former immediate, the latter delayed (possibly hormonal). It is further suggested that the former is a response to circulating intravascular volume expansion, possibly ‘sensed’ by stretch and/or pressoreceptors.


Complex variable techniques are used for the study of the electrohydrostatic stability of two dimensional charged conducting membranes, which are assumed to be fixed along their edges. The formulation of the problem is quite general, but the numerical solution presented refers to the case when the membranes are symmetrical with respect to the plane bisecting their width and carry equal and opposite charges. It is found, as expected, that for a given set of data the equilibrium configuration breaks down if the membranes are sufficiently charged. When the membranes are sufficiently apart the breakdown occurs at their edges and is manifested as inability of the system to satisfy the equilibrium conditions there. When the membranes are sufficiently close together and are charged to a certain level, they touch at their mid-points and the equilibrium breaks down. Our results are compared with an approximate solution of this problem, presented by two other authors. The approximate solution ignores the edge effects of the membranes and overestimates the amount of charge that the membranes can carry before breakdown occurs. In the special case when the gap between the membranes is much less than their width, our results are in quantitative agreement with the approximate solution but as the gap between the membranes increases, the accuracy of the approximate solution decreases.


2007 ◽  
Vol 61 (12) ◽  
pp. 1398-1403 ◽  
Author(s):  
Daewon Lee ◽  
Hyeseon Lee ◽  
Chi-Hyuck Jun ◽  
Chang Hwan Chang

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