\[ %\scriptsize {\sf Y}:= \left[ \begin{array}{c} {\sf y_1} \\ {\sf y_2} \\ \vdots \\ {\sf y_n} \end{array} \right] ~~~ {\sf X}:= \left[ \begin{array}{ccccc} \mathsf{x_{11}} & \ldots & \mathsf{x_{1j}} & \ldots & \mathsf{x_{1p}}\\ \mathsf{x_{21}} & \ldots & \mathsf{x_{2j}} & \ldots & \mathsf{x_{2p}}\\ \vdots & \ldots & \vdots & \ldots & \vdots \\ \mathsf{x_{n1}} & \ldots & \mathsf{x_{nj}} & \ldots & \mathsf{x_{np}}\end{array} \right] \]
\[ %\scriptsize \left[ \begin{array}{c} \mathsf{y_{1}} \\ \mathsf{y_{2}} \\ \vdots \\ \mathsf{y_{n}} \end{array} \right] \sim \left[ \begin{array}{c} \mathsf{x_{1j}} \\ \mathsf{x_{2j}} \\ \vdots \\ \mathsf{x_{nj}} \end{array} \right] ~~ \leadsto ~~ \left\{ \begin{array}{cl} \mathsf{\hat{\beta}_j}: & \textsf{marginal effect estimate} \\ \mathsf{\hat{\sigma}_j}: & \textsf{standard error of}~\mathsf{\hat{\beta}_j} \end{array}\right. \]
Select references: Moser et al. (2015); Loh et al. (2015); Bottolo et al. (2013); Zhou et al. (2013); Carbonetto & Stephens (2012); Guan & Stephens (2011); Kang et al. (2010); Logsdon et al. (2010); Yang et al. (2010); Hoggart et al. (2008); Wu et al. (2009); Servin & Stephens (2007).
Reference: Zhu & Stephens (2017, To appear). http://dx.doi.org/10.1101/042457
References: Wood et al. (2014); Zhou et al. (2013); Yang et al. (2011); Guan & Stephens (2011); Yang et al. (2010).
\[ \beta_{\sf j}\sim \pi_{\sf 0}\cdot \delta_{\sf 0} + {\textstyle \sum}_{\sf k=1}^{\sf K} \pi_{\sf k} \cdot {\sf N}({\sf 0}, \sigma^{\sf 2}_{\sf k}) \]
\[
\beta_{\sf j}\sim ({\sf 1}-\pi_{\sf j})\cdot \delta_{\sf 0} + \pi_{\sf j}\cdot {\sf N}({\sf 0}, \sigma^{\sf 2}_{\beta})
\]
\[
\textsf{log}_{\sf 10}[\pi_{\sf j}/(1-\pi_{\sf j})] = \theta_{\sf 0} + \theta \cdot {\sf 1}\{\textsf{SNP j}\in \textsf{gene set}\}
\]
\[
\beta_{\sf j}\sim {\sf N}({\sf 0}, \sigma^{\sf 2}_{\sf j})
\]
\[
{\sf log}(\sigma^{\sf 2}_{\sf j}) = {\sf w}_0 + {\textstyle \sum}_{\sf g=1}^{\sf G} {\sf w}_{\sf g} \cdot {\sf 1}\{\textsf{SNP j}\in \textsf{category g}\}
\]
Data source: http://csg.sph.umich.edu/abecasis/public/lipids2010 (Teslovich et al. 2010).
Recent reviews: de Leeuw et al. (2016); Pers (2016); Mooney et al. (2014); Wang et al. (2010).
Function
(Pathway, Phenotype)Select references for M1: Veyrieras et al. (2008); Carbonetto & Stephens (2013); Pickrell (2014); Kichaev et al. (2014); Chen et al. (2016); Li & Kellis (2016); Wen et al. (2017).
# of Parameters = 31 \(\times\) (3,913+113) \(\times\) 1.1 Million \(\approx\) 137 Billion
HDF5
)Software:
https://github.com/stephenslab/rss
Demonstration:
http://stephenslab.github.io/rss/Example-5
R
package (in progress):
https://github.com/stephenslab/rssr (N. Knoblauch)
Reference: Teslovich et al. (2010).
References: Global Lipids Genetics Consortium (2013); Teslovich et al. (2010).
References: Xi et al. (Submitted); Dey et al. (2017); The GTEx Consortium (2015); Lambert et al. (2013).
Barber & Candès (2015); Stephens (2017); Brzyski et al. (2017) …
Leek & Storey (2007); Sun et al. (2012); Risso et al. (2014) …
Liang & Wong (2000); Neal (2011); Hoffman et al. (2013) …
Park et al. (2010); Thompson et al. (2015); Speed et al. (2017) …
Nicolae et al. (2010); He et al. (2013); Pickrell (2014) …
Reference: Zhu & Stephens (2017, Submitted). https://doi.org/10.1101/160770
References: Boyle et al. (2017); Hasin et al. (2017); Javierre et al. (2016); Li et al. (2016); Richardson et al. (2016); Ritchie et al. (2015).
R
package development