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Merged
eeyangc merged 9 commits into from
Apr 7, 2018
Merged

update reproducibility and simcode #2

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d134541
Update estLatent.R
mingjingsi Jan 13, 2018
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Update README.md
mingjingsi Mar 30, 2018
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mingjingsi Mar 30, 2018
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Update README.md
mingjingsi Mar 30, 2018
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mingjingsi Apr 2, 2018
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6 changes: 3 additions & 3 deletions R/estLatent.R
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ assoc.SNP <- function(fit, FDRset = 0.1, fdrControl){
est$gamma[which(FDR <= FDRset)] <- 1
}
if (fdrControl == "local"){
est$gamma[which((1-fit$pi1) <= FDR.set)] <- 1
est$gamma[which((1-fit$pi1) <= FDRset)] <- 1
}
}
else if(length(fit) == 6){
Expand All @@ -28,7 +28,7 @@ assoc.SNP <- function(fit, FDRset = 0.1, fdrControl){
}
if (fdrControl == "local"){
est$gamma.stage1[which((1-fit$pi1.stage1) <= FDRset)] <- 1
est$gamma[which((1-fit$pi1) <= FDR.set)] <- 1
est$gamma[which((1-fit$pi1) <= FDRset)] <- 1
}
}
else {
Expand All @@ -49,7 +49,7 @@ assoc.SNP <- function(fit, FDRset = 0.1, fdrControl){
if (fdrControl == "local"){
est$gamma.stage1[which((1-fit$pi1.stage1) <= FDRset)] <- 1
est$gamma.stage2[which((1-fit$pi1.stage2) <= FDRset)] <- 1
est$gamma[which((1-fit$pi1) <= FDR.set)] <- 1
est$gamma[which((1-fit$pi1) <= FDRset)] <- 1
}
}

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8 changes: 7 additions & 1 deletion README.md
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Expand Up @@ -27,7 +27,13 @@ package?LSMM
References
==========

Jingsi Ming, Mingwei Dai, Mingxuan Cai, Xiang Wan, Jin Liu and Can Yang. LSMM: A statistical approach to integrating functional annotations with genome-wide association studies. 2017. Under review.
Jingsi Ming, Mingwei Dai, Mingxuan Cai, Xiang Wan, Jin Liu, Can Yang; LSMM: A statistical approach to integrating functional annotations with genome-wide association studies, Bioinformatics, 2018, bty187, https://doi.org/10.1093/bioinformatics/bty187


Reproducibility
==========

All the simulation results can be reproduced by using the code at [sim-LSMM](https://github.com/mingjingsi/sim-LSMM).


Development
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